USER MANUAL (2005Release) F. Eisenmenger, U.H.E. Hansmann
Contents
1. Subroutine HBOND Usage call hbond nml mhb ipr This subroutine determines the number mhb of the hydrogen bonds for the current conformation of the molecule and requires nml as input the index of the present molecule in current version of SMMP this variable has to be set to 1 The hydrogen bonds are printed out for ipr gt 0 subroutine HELIX Usage helix nhel mhel nbet mbet HELIX determines whether a residue is part of an a helix or sheet according to its backbone dihedral angles Y ranges defined in a PARAMETER statement and returnes the number of helical residues nhel the number of helical segments mhel and the corresponding quantities for G strand elements nbet and mbet Subroutine METROPOLIS Usage call metropolis eol acz weight The subroutine implements one Metropolis move for every dihedral angle and re quires as input a weight function weight eol and the energy eol of the present configuration It returns in the variable eol the energy of the configuration af ter nvr the number of non fixed dihedral angles updates acz accounts for the number of Metropolis moves were the proposed configuration was accepted Subroutine OUTPDB Usage call outpdb nml npdb The subroutine writes in the output file the coordinates of the atoms of given molecule The format is compatible with the standard data representation for mat of the Brookhaven P2. 0 1 phi 4 136 8 0 2 psi 5 19 1 0 2 omg 5 174 1 5 9 x1 5 52 9 0 1 x2 5 175 3 0 0 x3 5 179 9 0 0 x4 5 58 6 0 0 phi 5 163 4 0 2 pst 5 160 8 0 3 omt 5 179 8 0 2 Gradient 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 23 9 2 Structure Determination by Simulated Annealing For the following simulated annealing run for Met Enkephalin defined through its seguence file enkefa seg another configuration file enkefa ann is used By this configuration file omk 180 0 amp the dihedral angles omg and omt angles are all set to 180 0 degrees and fixed subsequently The reason for this choice is that simulated annealing performs only poorly for the case where these angles are free to change Simulated annealing is chosen as simulation task by replacing call minim 1 through call anneal in main In this example we further choose as force field ECEPP 2 setting sh2 true and no protein solvation interaction Hence we have the following settings for parameters in main f flex false sh2 true epsd false itysol 0 grpn nh2 grpc cooh iabin 1 Our simulated annealing run will consist of 100 Monte Carlo sweeps at highest temper ature 1000 K followed by 100000 sweeps in which the temperature is gradually lowered down to a final temperature of 100 K The progress of the
3. 10 5 5 2 01 1 31 4 48 0 0 0 1 10 6 4 2 52 1 03 4 43 0 0 0 1 34 Pre FO Oo 100000 1 2 0 50 20 39 5 47 0 0 0 0 100000 2 4 0 84 11 05 4 81 0 1 0 1 100000 3 3 1 26 10 28 5 16 0 0 0 0 100000 4 6 1 68 3 06 4 62 2 0 0 1 100000 5 1 2 01 4 01 4 75 1 0 0 1 100000 6 5 2 52 7 71 4 69 1 0 0 1 At the end of the simulation the final configurations are written into external files in our case enkefa oxx where xx marks the replica index Further information for re starts is written into par_R in that also collects statistics on the run 35 PR RORO
4. 161 6 1 phi 88 5 2 psi 153 2 2 omg 180 0 amp 2 phi 168 5 3 psi 87 3 3 omg 180 0 amp 3 phi 78 1 4 psi 70 1 4 omg 180 0 amp BL i 174 3 RI 127 1 4 phi 107 0 9 psi 48 7 b omg 180 0 amp 5 xl 67 6 5 x2 176 2 5 x3 177 9 5 x4 168 9 5 phi 159 4 25 5 pst 174 3 5 omt 180 0 amp lowest energy ever found 55794 9 61510136 Tis xb 173 7 1 82 28 112 3 1 Xx6 141 4 1 phi 74 2 2 psi 152 8 2 omg 180 0 amp 2 phi 161 7 3 psi 65 3 3 omg 180 0 amp 3 phi 70 2 4 psi 88 0 4 omg 180 0 amp 4 xi 178 2 Tt ee 76 5 4 phi 87 9 5 psi 29 9 5 omg 180 0 amp 5 xl 61 9 Be Per 171 5 5 x3 178 5 b x4 179 7 5 phi 79 8 5 pst 141 8 5 0 omt 180 amp The random start configuration final configuration and lowest energy configuration are also written in PDB format into the files start pdb final pdb and global pdb which allows an easy visualization of these configurations with programs graphically displaying PDB structures The progress of the simulated annealing run is monitored through the time series in file time d which list the Monte Carlo sweep temperature ECEPP 2 energy radius of gyration and the Zimmerman coding of the present configuration 0 1000 000 19 256 5 982 EfbE 1000 977 237 12 361 6 020 EeaA 2000 954 993 22 999 5 234 DFbA 3000 933 254 18 473 6 072
5. GAHD 4000 912 011 13 257 6 199 bDhF 5000 891 251 18 902 4 951 DBAF 6000 870 964 14 526 5 144 eDDB 7000 851 138 11 837 5 299 EhdE 8000 831 764 15 603 4 821 FDdC ND aD 99000 100000 812 794 125 123 120 117 114 112 109 107 104 102 100 831 328 893 027 226 490 815 202 648 152 713 329 000 10 19 447 689 295 203 452 705 123 227 126 658 066 839 561 SPA AA DR BR PB BOD 27 113 710 670 758 677 640 598 681 611 633 552 609 536 GAAF EddA FDcF FDcF FDcF EDcF FDcF EDcF FDcF EDcF EDCG FDCG FDcA 9 3 Calculation of Multicanonical Parameters In the following example multicanonical parameters are calculated for Met enkephalin with fixed omega angles in gas phase simulations relying on the ECEPP 3 force field For this purpose one has to replace in main line 50 call minim 1 through call mulcan_par and set the following parameters in main accordingly flex false sh2 false epsd false itysol 0 grpn nh2 grpc cooh iabin 1 The simulation has a total of 100 000 Monte Carlo sweeps and the multicanonical pa rameters are updated every 2 000 sweeps The parameters are calculated from scratch and we attempt to obtain a histogram in energy in the interval 12 20 Kcal mol with energy bin size 1 Kcal mol We expect that at temperature 1000 K we are clearly in the high en
6. In the current version of this requested through an interactive command line dialog issued by call init_molecule The user can easily just supply the corresponding file names in a here document as shown in the example scripts 7 At this point the program is ready for calling task subrotuines In the provided version of main the energy minimization subroutine is called through call minim Detailed examples for this and other simulation tasks can be found in the following 18 section Normally simulation subroutines write data in output files but one can also use output routines such as outpdb in main The minimal output written into standard output is the name of the sequence file extension seq name of configuration file extension var and for each residue a list of dihedral angles together with their initially assigned values For parallel tempering jobs on on a multiprocessor system one has to replace main by pmain The above protocol still applies but one has to provide in addition the number of nodes with the variable no 19 8 How to cite SMMP Use of SMMP should be acknowledged by guoting the following reference 1 F Eisenmenger U H E Hansmann Sh Hayryan C K Hu SMMP A Modern Package for Simulation of Proteins Comp Phys Comm 138 2001 192 212 2 F Eisenmenger U H E Hansmann Sh Hayryan C K Hu An Enhanced Ver sion of SMMP Open Source Software Pac
7. a brief description of the important routines and describes some limitations of the package A few example runs providing detailed explanation of input and output are added More information on SMMP definitions background and references for force fields and algorithms as used in the program package can be found in 1 2 SMMP is offered as open source code We encourage users to re write code or add their own modules This task is eased up by the simplicity of the programs written in standard FORTRAN As a courtesy to the authors and future users of SMMP we ask you to send us a note if you feel that your add on or your modification of SMMP would be useful for other users too The usage and distribution of the program are governed by the following license agreement By viewing or using any part of the program package SMMP you accept the following terms SMMP is free software it can be used modified and redistributed under the terms of the GNU General Public License http www gnu org licenses gpl html as published by the Free Software Foundation EXCEPT WHERE RESTRICTED BY ONE OF THE FOLLOWING CLAUSES The program may be only used in the context of scientific research and teach ing at a university or university like institution Its use for commercial and or military purposes or in the context of commercial and or military research is explicitly forbidden The use of SMMP has to be acknowledged in all resulting publications by quot
8. its rmsd and list of remaining bad contacts e Subroutine MINIM file minim f Usage call minim imin This subroutine minimizes the current configuration of the molecule It can be called from any point during the simulation once a configuration is defined When calling this subroutine one needs to specify the type of minimizer through variable imin Setting imin 1 chooses a Quasi Newton minimizer by calling mingsn min 2 a Conjugate Gradient minimizer mincjg The performance of these minimizers can be controlled by setting various parameters in MINIM such as the accuracy acc or the total number of function calls mxop see the header of MINIM for the various parameters that can be adjusted 12 e Subroutine CANON file canon f The subroutine carries out a canonical simulation at temperature temp which has to be assigned in a PARAMETER statement The simulation starts from a random configuration if the logical parameter lrand is set to TRUE Otherwise the simulation starts from the current conformation of dihedral angles as stored in array vlvr In separated PARAMETER statements one also has to set the number of Monte Carlo sweeps for the simulation nswp and at the equilibration negul as well as the number nmes of Monte Carlo sweeps between measurements Three output files are created files start pdb and final pdb are for storing the start and final configuration
9. pmain f and partem_p f These subroutines are used for parallel tempering simulations on a parallel computer with no nodes PMAIN replaces MAIN in this case Both PMAIN and PARTEM_P 14 6 2 utilize the MPI message passing routines The number of nodes no has to be set in both modules and eguals to the number of replicas in the parallel tempering method In addition one has to set in PARTEM P also the following variables the number of Monte Carlo sweeps for equilibration negui and simulation nsweep and the number of Monte Carlo sweeps between measurements nmes If not for re starts the logical variable newsta should be set to FALSE in which case all dihedral angles are set to the random values At the end of the simulation all dihedral angles are stored in the file par R in from which the program reads its start configurations if newsta TRUE Before running the program one has to prepare the file temp d with no lines Each line lists the index of replica j and its temperature temp In our template we measure every nmes Monte Carlo sweeps for each replica a number of quantities the radius of gyration rgy the number of residues nhel and segments mhel in an a helix the number of residues in a P sheet nbet and the number of such segments mbet the number of hydrogen bonds mhb and the number of contacts nctot and native contacts ncnat The late
10. section of init_energy f SMMP employs 9 different sets of atomic solvation parameters We do not include references to the original works where these sets are defined in this document since this manual is only a supplement to our articles 1 2 where all relevant references can be found The set of solvation parameters chosen is indicated by the value of integer variable itysol in the MAIN module If setting itysol to a positive value between and 9 in MAIN the numerical method enysol is applied to compute the solvation energy term By choosing a negative integer value for itysol from the interval 1 9 the analytical method esolan is used to calculate the solvation energy The tesselation points for numerically calculating the solvent accessible surface area have to be provided in an external file named tes dat in our package and read in during initialization of solvation parameters in init_energy f 5 Input Files SMMP reguires an input file ithat specifies the seguence of amino acid residues of the protein in plain ASCII format Note that because of limitations in the present version of SMMP only one molecule may be specified 5 1 PDB File Setting the variable tabin 0 in main f the sequence of amino acids is read from a PDB file the standard format in which protein structures are deposited in the Protein Data Bank The atomic coordinates are also read from the PDB file and can serve as a start configuration However on
11. 2 N CA C phi 120 If a molecule consists of n residues then pst defines dihedral N n CA n C n Oxt n omt defines dihedral CA n C n Oxt n Hxt n Oxt amp Hxt comprise the hydroxyl of the C terminal carboxyl group The following example configuration file enkefa var is provided with the program and may be used with the sequence file enkefa seq a aaa ala enkefa var 1 Los xl 172 59 a SG 78 71 1 x6 165 88 2 psi 156 18 2 omg 180 00 2 phi 154 53 3 psi 83 64 3 omg 180 00 3 phi 83 66 4 psi 73 86 4 omg 180 00 4 phi 137 04 4 xi 58 79 4 x2 94 60 5 psi 19 33 5 omg 180 00 5 phi 163 63 5 5 5 5 5 5 11 6 Frequently used Functions and Subroutines 6 1 Task Subroutines In the following we describe some important simulation subroutines and their reguisites For more information see 1 2 Following the philosophy behind SMMP these routines are rather simple and may serve as templates which the user can modify according to his special needs e Subroutine REGUL file regul f Usage call regul nml For a given PDB structure the actual bond lengths and bond angles generally differ from those in the standard geometry model assumed with the ECEPP or FLEX potential This subroutine is applied to determine the configuration within the standard geometry that is as close as possible to a given PDB structure
12. 2018 5 7730721 OR OO OO OOOO One 847746885 138656239 654146664 644605311 553037646 474305513 490066347 409995341 422133779 422133779 422133779 69162077 49162366 47750877 35347117 07152387 890541874 14271521 218491892 08246745E 15 55111512E 16 A test simulation of 100 000 Monte Carlo sweeps using subroutine mulcan_sim with these weights led to the following histogram that is flat over the studied energy range as is characteristic for the multicanonical ensemble note that the last energy bin contains all entries for energies larger egual than 20 Kcal mol 12 0 11 0 10 2515 9 1005 8 1036 7 1014 6 1113 5 1200 4 1549 3 2193 2 2665 1 2923 0 2901 1 3098 29 O ON DOP WD r E HO NGE HR HEEE RE OO ON MT P ON 3120 3025 3083 3183 3216 3122 3170 3261 3338 3340 3307 3515 3434 3585 3613 3538 3462 3315 17147 30 9 4 Regularization of the B domain of protein A Freguently one wants to compare the results of a simulation with experimental data When comparing properties of calculated configurations with that of structures from the Protein Data Bank PDB one has to remember that the actual bond lengths and angles in the PDB structure will slightly differ from the fixed values that are assumed with the ECEPP or FLEX potentials Forcing the molecule into the standard bonding geometry model of ECEPP or FLEX may le
13. 518E 07 0 866791E 10 Step 425 energy 0 430829E 03 0 158450E 07 0 866791E 10 Step 426 energy 0 430829E 03 0 894306E 09 0 866791E 10 32 Step 427 energy 0 430829E 03 0 143664E 09 0 866791E 10 Step 428 energy 0 430829E 03 0 143664E 09 0 866791E 10 CONVERGENCE Final energies Total 0 43083E 03 Coulomb 0 5354E 02 Lennard Jones 0 3531E 03 HB 0 7209E 02 Variables 0 4795E 02 Solvatation 0 0000E 00 Regularization 0 5382E 04 RMSD 1 75752506 Dihedral angles of 84 65 the regularized structure 1 xi 1 x2 1 x3 1 x4 1 phi 46 psi 46 omg 46 xi 46 phi 46 pst 46 omt 178 33 9 5 Parallel Tempering simulation of Met enkephalin In the following example a Parallel Tempering simulation of Met enkephalin in gas phase is performed that relies on the ECEPP 3 force field and where all dihedral angles are free References for the algorithm can be found in 1 The simulation is performed on a parallel computer and 6 nodes are used It is best to use a separate Makefile named Makefile p in our program distribution in which one has to set the correct compiler and linker option for the MPl installation of the specific parallel computer Note that the main program is no longer main but pmain in which one now has to set the following parameters accordingly no 6 flex false sh2 false epsd false itysol 0 grpn nh2 grpc cooh Afte
14. 83 energy 0 124285E 02 Step 84 energy 0 124285E 02 Step 85 energy 0 124285E 02 Step 86 energy 0 124285E 02 CONVERGENCE OO MEET PEN DEN BEN EN ER EN ANAN EN EN EN SS O OOO OO O nn an BB ir DA A Ww Go OOOO OOOO O 22 Gly Phe Phe Phe Phe Phe Met Met Met Met Met Met Met Met Met 0 1142E 03 HB phi psi omg xi x2 phi psi omg xi x2 x3 x4 phi pst omt set set set set set set set set set set set set set set set 0 0000E 00 137 179 163 867243E 13 964364E 07 498256E 04 109979E 05 678892E 09 143880E 05 100364E 05 172508E 04 105718E 04 580821E 03 Not Ne ON a OR NA ON Se NA 370905E 08 324300E 08 177363E 09 443358E 10 322695E 11 144369E 11 322695E 11 NA NGA NGA NGA NI u NG 83 73 180 58 94 660 860 000 790 600 040 330 000 760 280 830 570 630 450 000 19 180 52 175 58 160 180 0 9008E 03 Final Ai a II II Ka a ET a II u Total 0 12429E 02 Coulomb 0 2143E 02 Lennard Jones 0 2923E 02 HB 0 6706E 01 Variables 0 2084E 01 Solvatation 0 0000E 00 Variables _________________ zi 1 173 2 0 6 x2 1 79 3 0 6 x6 1 166 3 0 5 phi 1 83 1 3 2 psi 2 155 8 0 4 omg 2 177 1 2 9 phi 2 154 2 0 3 psi 3 85 8 2 2 omg 3 168 5 11 5 phi 3 83 0 0 7 psi 4 75 0 1 2 omg 4 170 0 10 0 zi 4 58 9 0 1 x2 4 94 5
15. SMMP USER MANUAL 2005 Release F Eisenmenger U H E Hansmann Sh Hayryan C K Hu CONTENTS 1 INTRODUCTION 2 INSTALLATION 3 LIMITATIONS 4 LIBRARIES AND PARAMETERS 5 INPUT FILES a PDB File b Sequence File c Configuration File Dihedrals 6 FREQUENTLY USED FUNCTIONS AND SUBROUTINES 7 HOW TO RUN SMMP 8 HOW TO CITE SMMP 9 EXAMPLES a Minimization of vacuum energy from a given configuration a b Structure determination by Simulated Annealing c Calculation of multicanonical parameters d Regularization of the B domain of protein A e Parallel Tempering simulation of Met enkephalin 1 Introduction The SMMP Simple Molecular Mechanics for Proteins package is designed for molecular simulations of linear proteins within the standard geometry model The package contains various modern Monte Carlo algorithms and energy minimization routines The energy of a protein can be calculated by exploiting one of three force fields ECEPP 2 ECEPP 3 or FLEX Two subroutines for approximating protein solvent interactions by means of calculating the solvent accessible surface area of atomic groups are included Nine sets of solvation parameters are available All calculations are done with double precision but the user can easily modify this option by changing the corresponding IMPLICIT statement This manual provides the user with the necessary information for installation of the program to format input and output files
16. ad to un physically high energies The process of finding an optimal structure within the standard geometry model starting rom a PDB structure is called regularization Our example we concentrate on the regularization of the atom coordinates for residues 10 55 of the B domain of Staphylococcus Aureus Protein A which were taken from entry IBDD of the Protein Data Bank see http www rcsb org as provided with this package in file 1bdd pdb in sub directory EXAMPLES Setting the variable iabin 0 in main f makes init_molecule call subroutine pdbread that reads the amino acid sequence and the atomic coordinates rom the PDB structure and stores this data in arrays declared in INCP H Then pdbvars is automatically called to measure all dihedral angles In order to regularize the PDB structure one has to call regul 1 as the task subroutine in main replacing call minim 1 as provided with program package Set the following parame ters in main accordingly flex false sh2 false epsd false itysol 0 grpn nh2 grpc cooh iabin 0 Note that regul as any other task subroutine has to be called AFTER init_molecule and that nml has to be set to 1 in the present version of SMMP Re compile and link the package with this modified main f and use the following script i e file smmp reg in sub directory EXAMPLES cd smmp lt lt EXAMPLES 1bdd pdb First regul obtains its i
17. e should remember that the fixed bond lengths and angles with ECEPP or FLEX potential will slightly differ from the actual bond lengths and angles in the PDB structure Forcing the molecule into standard bonding geometry corresponding to a given potential may lead to un physically high energies Regularization through regul f allows to obtain an optimized structure with standard bonding geometry with low internal energy without differing significantly from the PDB structure 5 2 Sequence File Setting zabin 1 the amino acid sequence is read from a separate sequence file Its first line must start with a and may contain the name for the molecule The residues in the following lines should be named as in the library files lib sh2 lib sh3 or lib flex Residue names are not case sensitive and should be separated from each other by at least one white space Currently the following residue types can be used in SMMP 1 Neutral ala arg asn asp cys gln glu gly his hise hyp ile leu lys met phe prok ser thr trp tyr val where the residues marked by an asterix are characterized by his hydrogen at N delta atom hise hydrogen at N epsilon atom pro hyp down puckering 2 Charged arg asp glu his lys 3 Variants only with ECEPP 3 parameters hypu prou up puckering cpro cpru cis Pro with down up puckering pron pro N terminal neutral charged with respect to NH2 Pro End groups
18. e with FLEX parameters File with charges needed only for FLEX File with tesselation points for approximating the solvent accessible surface area of atoms Produces the executable file sequential jobs Produces the executable file for Parallel Tempering jobs on multiple processor machines Defines global parameters and common blocks Defines parameters and common blocks necessary for reading PDB structures Wrapping function that constructs the start configuration of a molecule Wrapping function that initializes the energy parameters Reads sequence of amino acids e g enkefa seq Reads initial configuration of molecule e g enkefa var Assembles data from libraries Builds up the protein atom coordinates Adds end groups Determines sets of moving atoms for given variables Compiles lists of interaction partners Resets variables and rebuilds the molecule Returns dihedral angles and valence angles 4 difang f nursvr f redstr f pdbread f energy f enyflx f enyshe f enysol f esolan f enyreg f gradient f opeflx f opeshe f opesol f opereg f main f regul f anneal f canon f minim f mulcan_par f mulcan_sim f partem_s f partem_p f pmain f metropolis f mingsn f mincjg f Calculates the difference and the sum of two dihedral angles Calculates the residue index of a dihedral angle or atom String input routines Reads amino acid sequence and atomic coordinates from a PDB file calculates dihedral angles
19. emia Sinica Taipei and by the National Science Council of the Republic of China Taiwan under Contract No NSC 89 2112 M 001 084 2 Installation The complete SMMP package is written in standard FORTRAN 77 language We have been exploiting it using the standard Gnu g77 and the Intel Fortran compiler for Linux but it should be possible to compile and link the code with any contemporary FORTRAN compiler All subroutines are stored in files f and an example Makefile is included in the package There are no machine dependent routines included in SMMP All COMMON blocks and the limiting parameters are gathered in INCL H which is attached to the necessary modules through an INCLUDE statement After uncompressing and unpacking via tar xvf command the SMMP package into a separate directory the following files can be found in that directory README SMMP manual pdf license txt lib sh2 lib sh3 lib flex charges tes dat Makefile Makefile_p INCL H INCP H init_molecule f init_energy f redseq redvar getmol bldmol addend setmvs mklist setvar dihedr f Fh bh FH FH FR bh EFA A A README file A sub directory containing The manual in PDF format describing the details of various subroutines and the installation of SMMP Ascii file with the license agreement Library file with ECEPP 2 parameters Library file with ECEPP 3 parameters Library fil
20. ergy phase where successive configurations are little correlated This leads to the following setting of parameters in subroutine mulcan par parameter l_iter false parameter kmin 12 kmax 20 ebin 1 0d0 parameter nsweep 100000 nup 5000 parameter temp 1000 0 After compilation of SMMP with the make command and running the program using the script smmp cmd the calculated multicanonical parameters are written into the file muca d For further iteration of these parameters additional quantities such as the accumulated histogram are written into a file mpar_full d out of which mulcan_par reads them if Liter true is set We show here only the file muca d which lists the index of the energy bin the 0 E and the a E parameters see 1 for more detailed explanations and references on multicanonical simulations 12 7 99001526 41 8549769 11 7 99001526 41 8549769 10 7 99001526 41 8549769 9 4 16266162 7 40879417 8 3 1249691 0 892745986 7 2 44799324 5 63157705 6 2 25973519 6 76112535 5 1 98376871 8 14095772 28 OANA UI UN Ho E E HO NGE HR HEEE E E ODO ON OA AF W ND OO HR HERE RRP BE 1 80583549 8 85269062 1 69241238 9 19295995 1 65228855 9 27320761 1 60274413 9 32275203 53176311 9 32275203 47795021 9 26893914 42184662 9 15673195 2908957 8 76387918 24563637 8 58284188 15611832 8 13525162 15781701 8 14544378 01678513 7 15822063 953895628 6 65510459 85589
21. espectively The file charges is needed for N and C terminal residues with FLEX parameters The name of the directory containing these 4 files should be given in string libdir which is assigned in module MAIN The choice between parameter sets for potentials ECEPP 2 and ECEPP 3 is done by the logical variable sh2 The potential FLEX is set by the logical variable flez The amino acid residue libraries contain chemical and structural data for each residue according the IUPAC IUB nomenclature The library files consist of blocks of records with each block representing one residue The first line in each block starts with a and contains the name of the residue and its total number of atoms Each following line within the block describes one atom Listed are its name the bond length and the valence angle to construct this atom the type and the name of corresponding torsion angle the partial charge for the atom the type of the atom as well as the previous and the following atoms max 3 it is connected to The atom and torsional parameters in the libraries are the same as in the original ECEPP 2 3 and FLEX potentials However it should be noted that SMMP has its own numeration of the atom types and the types of torsions see 1 2 for more details The arrays with the parameters for non bonded pairwise potentials Van der Waals hydrogen bonds electrostatic and the atomic solvation parameters are stored in the BLOCK DATA
22. f this module requires the preparation of a file reference d with the contact matrix of the target structure Subroutine PARTEMS file partem_s f This parameterless subroutine is designed to simulate a protein by means of the parallel tempering technique on a single processor Before running a parallel tem pering simulation using PARTEM_S one has firstly to set the following variables in this subroutine the number of replicas no and the initial temperatures on each replica array temp no the sum of the number of degrees of freedom over all replicas nvrmax the number of Monte Carlo sweeps at equilibration nequi and the number of Monte Carlo sweeps in between measurements nmes If not for re starts the logical variable Istart should be set to FALSE in which case all dihedral angles are set to random values At the end of the simulation all di hedral angles are stored in the file startconf d from which the program reads its start configuration if Istart TRUE In the simulation measurements are made every nmes Monte Carlo sweeps In our template we measure for each replica the radius of gyration rgy and the end to end distance ee by means of subroutine RGYR and write both values together with the temperature temp0 total energy energy Monte Carlo time nsw and the index of the replicas kl to an output file time d PMAIN and subroutine PARTEM P files
23. from PDB coordinates and builds index field that relates PDB atoms to SMMP atoms Wrapping function that returns the energy of a current protein configuration Calculates internal energy of molecule with FLEX dataset Calculates internal energy of molecule with ECEPP datasets Calculates solvation energy of molecule using solvent accessible area method fast but approximate calculation Calculates solvation energy of molecule using solvent accessible area method analytic but slow calculation Calculates a constraint energy needed for regularizing PDB structures Wrapping function that returns the energy gradient vs dihedral angles for a protein configuration Calculates internal energy and partial derivatives vs dihedral angles for FLEX dataset Calculates internal energy and partial derivatives vs dihedral angles for ECEPP datasets Calculates analytical partial derivatives vs dihedral angles of the solvation energy Calculates the partial derivatives vs dihedral angles of the constraint energy term during regularization Main program Regularization of PDB structure into SMMP geometry For simulated annealing run For canonical Monte Carlo run For minimization of protein potential energy Calculates multicanonical weights For multicanonical simulation run For parallel tempering run on a single processor machine For parallel tempering run on a multiple processor machine Replaces main f on multiple processor machine in paral
24. has to be re compiled We recom mend that new users spend some time studying the structure of the main init energy init_molecule and INCL H before start using SMMP The following steps summarize how to run SMMP 1 Assign to the character variable libdir the path to the directory containing the standard amino acid residue libraries and the file charges 2 Select the force field and solvation model by setting the four paramters flex sh2 epsd and itysol to their appropriate values x flex TRUE Flex potential flex FALSE ECEPP potential sh2 TRUE ECEPP 2 potential sh2 FALSE ECEPP 3 epsd TRUE Distant dependent dielectric permittivity epsd FALSE epsilon 2 x itysol 0 gas phase itysol gt 0 approximation of protein solvent interactions by means of a solvent accessible surface area approach with numerical estimation of the accessible area itysol lt 0 same as above but the accessible area is calculated analytically considerably than itysol gt 0 3 call init_energy libdir to initialize the energy parametrization 4 Choose the N terminal and C terminal groups by assigning to appropriate strings to variables grpn and grpc 5 Choose how the initial input is read in 0 read from PDB file 1 read from sequence and configuration file jabin jabin 6 Enter the names of the corresponding file s segfil and varfil
25. idue 1 Tyr x6 set 165 880 redvar gt Met Enkephalin residue 1 Tyr phi set 86 240 redvar gt Met Enkephalin residue 2 Gly psi set 156 180 redvar gt Met Enkephalin residue 2 Gly omg set 180 000 redvar gt Met Enkephalin residue 2 Gly phi set 154 530 redvar gt Met Enkephalin residue 3 Gly psi set 83 640 redvar gt Met Enkephalin residue 3 Gly omg set 180 000 No j redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt redvar gt Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin Met Enkephalin residue residue residue residue residue residue residue residue residue residue residue residue residue residue residue Energy BEFORE minimization Total 0 10354E 04 Coulomb 0 1991E 02 Lennard Jones Variables 0 4511E 00 Solvatation Step 1 energy 0 489976E 05 Step 2 energy 0 108241E 03 Step 3 energy 0 632755E 00 Step 4 energy 0 739539E 01 Step 5 energy 0 517957E 03 Step 6 energy 0 767774E 01 Step 7 energy 0 818570E 01 Step 8 energy 0 938401E 01 Step 9 energy 0 109799E 02 Step 10 energy 0 116244E 02 Step 80 energy 0 124285E 02 Step 81 energy 0 124285E 02 Step 82 energy 0 124285E 02 Step
26. ine MULCAN SIM file mulcan_sim f This subroutine performs a Monte Carlo simulation a protein using multicanonical weights Information necessary for a re start chosen by setting restart TRUE otherwise the simulation starts from a random configuration are saved after every nsave Monte Carlo moves into the file start d Parameters ebin kmin and kmax set the energy bin size and the lower and upper limits of the energy interval within which the multicanonical parameters were defined see MULCAN PAR These parameters are read from the file muca d and have to be the same as the ones used in MULCAN PAR to generate the multicanonical weights Other parameters which one has to initialize are the total number of Monte Carlo sweeps nsweep the number of Monte Carlo sweeps nequi needed for equilibration and the number of Monte Carlo sweeps nmes between successive measurements In our example the output goes to file time d in which the time series of the simulation is written Measured quantities are the total potential energy eol the number of contacts nhx and the number of native contacts nhy7 The latter number counts for the contacts which are same in the present configuration and the target structure Also measured is the Hamming distance dham between the present and the target configuration The latter three quantities are calculated by the subroutine CONTACTS A call o
27. ing F Eisenmenger U H E Hansmann 5 Hayryan and C K Hu SMMP A Modern Package for Protein Simulations Comp Phys Comm 138 2001 192 212 An Enhanced Version of SMMP Open Source Soft ware Package for Simulation of Proteins submitted No part of SMMP shall be incorporated into other programs without explicit 2 permission of the authors SMMP is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details The most recent version of SMMP can be found on the program package s web sites http www smmp05 net or http www phy mtu edu biophys smmp htm Any suggestions for improvements of the code or reports on bugs are welcome Please send your remarks to Frank Eisenmenger Forschungsinstitut fur Molekulare Pharmakologie 13125 Berlin Germany E mail eisenmenger fmp berlin de Ulrich H E Hansmann Michigan Technological University Houghton MI 49931 1291 USA E mail hansmann mtu edu Shura Hayryan Institute of Physics Academia Sinica Nankang Taipei 11529 Taiwan E mail shura phys sinica edu tw Chin Kun Hu Institute of Physics Academia Sinica Nankang Taipei 11529 Taiwan E mail huckOphys sinica edu tw Acknowledgments U H acknowledges support by a research grant CHE 9981874 of the National Science Foundation USA S H and C K H are supported by Acad
28. kage for Simulation of Pro teins submitted 3 Where appropriate the program package s web site should be guoted as http www smmp05 net 20 9 Examples 9 1 Minimization of vacuum energy rom a given configuration The example MAIN module has the following settings flex false sh2 false epsd false itysol 0 grpn nh2 grpc cooh iabin 1 which restricts energy calculations to evaluation of the ECEPP 3 energy no protein solvent interactions taken into account choses nh2 as N terminal group and at the C terminus the cooh group and finally states that the input is read from a sequence configuration file The the simulation task subroutine is called in our example call minim 1 i e the simulation task is the local minimization of the vacuum energy of a configuration using the Quasi Newton algorithm After setting the directory path in variable libdir and compilation SMMP with this default settings will minimize the configuration given in enkefa var using the following script file smmp cmd in sub directory EXAMPLES cd smmp lt lt EXAMPLES enkefa seq EXAMPLES enkefa var Running SMMP with this script will lead to the following output file with SEQUENCE EKAMPLES enkefa seg file with VARIABLES EXAMPLES enkefa var redvar gt Met Enkephalin residue 1 Tyr x1 set 172 590 redvar gt Met Enkephalin residue 1 Tyr x2 set 78 710 redvar gt Met Enkephalin res
29. lel tempering runs Performs Metropolis updates Minimization by quasi Newton method Minimization by Conjugate Gradient method outvar f contacts f cnteny f hbond f helix f outpdb f rgyr f zimmer f rmsdfun f EXAMPLES enkefa enkefa enkefa enkefa enkefa seq var ann ref temp smmp cmd 1bdd pdb smmp reg Output of the current conformation Calculates van der Waals contacts Calculates atomic contact energy and prints bad contacs Calculates number of hydrogen bonds in a configuration Measures the number of residues which are part of alpha heli or beta sheet Output of current configuration in PDB format Measures the radius of gyration and end to end distance in a molecule Expresses given configuration in Zimmerman code Calculates root mean square deviation between current SMMP configuration and a reference structure A sub directory containing Example sequence file Example configuration file Example configuration file for simulated annealing run Example contact matrix file Example temperature file for parallel tempering runs Example shell script to run smmp Example PDB file for regularization Example shell script to run smmp for regularization For the installation of SMMP the user needs to apply the Makefile in the directory with the sorce code One may edit this Makefile and customize the compiler command and compiler options to be used Executing the command make will co
30. les of the final structure are printed out together with its rmsd and a list of eventually remaining bad contacts The following output is obtained from this last iteration with a weight of 1 for the ECEPP energy and a weight of 0 for the constraint energy that leads to a SMMP configuration with a total ECEPP energy of 430 8 kcal mol and a rmsd of 1 76 AA compared to the PDB structure Energy BEFORE minimization 0 3407E 02 Total 0 40128E 03 Coulomb 0 4687E 02 Lennard Jones 0 3315E 03 HB 0 6948E 02 Variables 0 4654E 02 Solvatation 0 0000E 00 Regularization Step 1 energy 0 133729E 16 0 174001E 37 0 333203E 12 Step 2 energy 0 363055E 04 0 368838E 12 0 989962E 11 Step 3 energy 0 274981E 03 0 648848E 08 0 274633E 11 Step 4 energy 0 333018E 03 0 379334E 09 0 889472E 09 Step 5 energy 0 399762E 03 0 582647E 06 0 398837E 08 Step 6 energy 0 401426E 03 0 194084E 05 0 100221E 08 Step 7 energy 0 401658E 03 0 309779E 05 0 129744E 08 Step 8 energy 0 402059E 03 0 181490E 05 0 213119E 08 Step 9 energy 0 402563E 03 0 172799E 06 0 772566E 08 Step 10 energy 0 402764E 03 0 330004E 06 0 164070E 09 Step 420 energy 0 430829E 03 0 962300E 04 0 866792E 10 Step 421 energy 0 430829E 03 0 122085E 04 0 866791E 10 Step 422 energy 0 430829E 03 0 305390E 05 0 866790E 10 Step 423 energy 0 430829E 03 0 579932E 06 0 866791E 10 Step 424 energy 0 430829E 03 0 633
31. mperature temp the total energy eol the radius of gyration rgy as calculated by subroutine RGYR and the Zimmerman code as character variable zimm of the present configuration as obtained through subroutine ZIMMER e Subroutine MULCAN PAR file mulcan_par f This subroutine calculates multicanonical weight factors and has two working modes One is for improving the already existing set of multicanonical parameters through further iterations and the another is to calculate them anew In the first case the logical variable liter is set to the value TRUE and the input information is the histogram from a preliminary simulation as well as the existing values of the parameters are read from the file mpar_full d In the second case Liter FALSE all these arrays are initialized to zero In PARAMETER statements lower and upper limit gt kmin and kmax of the energy range and the size of the energy bin ebin have to be set Other parameters which one has to set are the total number of Monte Carlo sweeps nsweep the number of Monte Carlo sweeps nup in between updates of multicanonical parameters and the temperature temp of the initial canonical simulation Every nup sweeps the histogram of the preliminary 13 simulation as well as the ezisting values of the parameters are written to the file mpar full d The final multicanonical parameters are written into the file muca d Subrout
32. mplete the installation of SMMP 3 Limitations All parameters which limit the usage of SMMP are stored in the file INCL H The most important ones are listed below The values of these parameters should be changed only in a consistent way mxml 1 mxrs 100 mxat 2000 mxbd 3 mxvr mxrs b mxms mxvr 3 mxvw mxat 4 mx14 mxat 4 mxath 100 mxvrh mxath mxtyat 18 mxhbdo 4 mxhbac 6 mxtyto 19 nrsty 35 mxtysol 9 max max max max max max max max max max max max max max max the number of molecules total number of residues total number of atoms number of bonds to following atoms number of local variables total number of moving sets number number number number number of of of of of vdw domains 1 4 partners atoms in help arrays variables in help energetic atom types types of Hydrogens as donors in HB types of atoms as acceptors in HB number of types of torsional potentials number of residue types number of solvation parameters sets Note also the following restrictions in the current version of SMMP 1 Only single molecules can be studied therefore the parameter MXML must be always set equal to 1 2 A single amino acid residue can not be simulated with the FLEX potential 3 A protein must not start with a prolyl residue A Libraries and Parameter Files The residues which can be used with each parameter set are described in files lib sh2 lib sh3 and lib flex r
33. need to be specified in main f and are added through subroutine addend to the N and C terminus correspondingly At present molecules with only one single residue cannot be simulated with the FLEX data set and the first residue should not be a prolyl residue An example seguence file provided with SMMP may look as follows Fester Sse sss esse enkefa seg gt 3 572 gt 7222 7 Met Enkephalin Tyr Gly Gly Phe Met 5 3 Configuration File Dihedrals With option iabin 1 SMMP allows to provide a designated start configuration by listing dihedral angles in a second input file If no name of any configuration file is given or the name of a non existing file is entered all variables retain their default values as defined in the libraries This configuration file has to follow a fixed structure in which each line can be con sidered as a COMMAND for subroutine redvar The following syntax has to be used in each COMMAND RESIDUE VARIABLE VALUE Hence each line can consist of up to 3 FIELDS separated by an In the first field the RESIDUE is selected through an INTEGER number which marks its position in the amino acid sequence The second field should contain a string with the name of the VARIABLE i e names the specific dihedral angle The last field provides the value for the VARIABLE a REAL number and is mandatory A symbol amp following this number indicates that the variable will be fixed to that value thro
34. nput from the arrays declared in INCP H In a first step a naive representation of the molecule is build in the ECEPP geometry rom the stored dihedral angles that were calculated from the PDB coordinates This simple model serves as start configuration for the regularization In our example its root mean sguare deviation over all heave atoms compared to the PDB structure initially is 2 8 and its ECEPP energy 109 kcal mol mainly due to excessive van der Waals repulsions The regularization 31 starts by first minimizing a term that measures the sum of sguared distances between heavy atoms in the SMMP structure and the given PDB structure This leads to a rmsd of 0 14 kcal mol After this initial step a list of bad contacts vdW energy of more than 2 kcal mol in the SMMP structure is printed out In a second step the physical energy is minimized allowing only the free hydrogens to move and the bad contacts and rmsd are displayed again This step reduces the ECEPP energy to 10 kcal mol Regul aims at further reducing this energy while at the same time keeping the rmsd as small as possible This is done by minimizing a composite energy from the weighted sum of physical ECEPP energy and constraint energy the guadratic distance measure over 10 iterations In each iteration the weight of the constraint energy is successively lowered from 1 to 0 and the weight of the ECEPP energy raised from 0 to 1 At the end the dihedral ang
35. ole for an atom Functions ENERGY ENYSHE ENYFLX ENYSOL ESOLAN and ENYREG Usage eny energy The real 8 function energy is a wrapping function that calculates the energy of a 15 given configuration Depending on the choice of parameters flex sh2 itysol and reg in main pmain the vacuum energy of the protein is calculated by the functions enyshe ECEPP 2 or ECEPP 3 or enyflex FLEX and the solvation energy using the solvent accessible area method with enysol approximate but fast estimation of the solvated area or esolan analytical but slower calculation of the area enyreg calculates the constraint energy term needed during regularization of PDB structures energy returns the sum of these energy terms as selected by the parameters in the main module Subroutine GRADIENT OPESHE OPEFLX OPESOL and OPEREG Usage call gradient The wrapping subroutine gradient calculates the energy and partial derivatives with respect to internal degrees of freedom for a given protein configuration De pending on the choice of parameters flex sh2 itysol and ireg the subroutines opeshe ECEPP 2 or ECEPP 3 opeflz FLEX opesol solvent accessible sur face area and or opereg constraint energy term during regularization of PDB structures are selected and contribute to the total energy and its gradient that is calculated
36. r number counts the contacts which are same in the present configuration and in the target structure For this one has to prepare in advance the file reference d with the contact matrix of the target structure All measured quantities are written together with energy temperature and the index of the corresponding replica in the file ts d At the end of the simulation the average energy and specific heat for each temperature replica and the acceptance rate of replica exchange moves are written to standard output Useful Subroutines Subroutine CONTACTS Usage call contacts ncn nham2 dham This subroutine calculates the matrix of the van der Waals contacts between C atoms for a given configuration ncn is the total number of such contacts nham2 the number of native contacts i e such con tacts which are the same in the present configuration and the reference configuration and the Hamming distance dham between the present and the target configuration Subroutine CNTENY Usage call cnteny nml The subroutine cnteny displays a list of heavy atoms in molecule nm that have a contact energy of more than 2 kcal mol If one sets the parameter ieyel 0 in enteny the the contact energy is calculated with the van der Waals energy term only Setting ieyel 1 additionally includes the electrostatic energy into the contact energy and bad contacts are displayed if this energy exceeds a value of 10 kcal m
37. r reading the amino acid sequence and start configuration and initialization by means of calling init_energy and p_init_molecule pmain calls partem_p which does the parallel tempering simulation The subroutine reads as input the distribution of temperatures and for measuring purposes a map of contacts from external files in our example enkefa temp and enkefa ref in sub directory EXAMPLES that have to be provided In our example the simulation starts from random configuration with 10 000 sweeps for equilibration The molecule is then studied over 100 000 sweeps on each node with measurements taken every 10 sweep Hence the following parameters have to be set parameter nequi 10 nswp 1000 nmes 10 parameter newsta true After compilation Makefile_p the program is ready to run We do not provide a script as its form depends on the specific MPI installation The data are written into a file ts d In our case the data are the sweep the temperature index the index of the replica with that this temperature is currently associated the inverse temperature and energy radius of gyration number of residues that are part of a helix or sheet number of hydrogen bond total number of contacts and the number of contacts that appear also in the reference configuration 10 1 3 0 50 12 97 5 68 0 2 0 0 10 2 2 0 84 16 00 6 46 1 0 0 0 10 3 6 1 26 4 14 4 92 3 1 0 1 1 4 1 1 68 4 79 4 74 0 1 0 1
38. rotein Data bank This subroutine requires as input the 16 index nm of the given molecule has to be equal to 1 in the present version of SMMP and the logical unit number npdb of the output file Subroutine OUTVAR Usage call outvar nml iswitch This subroutine writes the dihedral angles of the current configuration of molecule nm to either standard output iswitch lt 0 or a dedicated file iswitch gt 0 where iswitch is the logical unit number of the file The dihedral angles are written out in a form that allows to use them as configuration input file for SMMP Function RAND Our package does not include a random generator Hence the user has to pro vide a random generator for calculating random numbers uniformly distributed in the interval 0 1 and has to modify accordingly the subroutines METROPOLIS CANON ANNEAL MULCAN_PAR MULCAN_NEW PARTEM_S PARTEM_P and ESOLAN In the provided versions of these subroutines we have assumed that the default FORTRAN random generator is used which however may cause some systems problems Subroutine RGYR Usage call rgyr nml rgy ee This subroutine calculates the radius of gyration rgy and the end to end distance ee for the protein molecule nml Both quantities characterize the compactness of a protein conformation Function RMSDFUN Usage rmsd rmsdfun nml ir1 ir2 ixat rrf yrf zrf isl The real 8 function rmsdfun calculates the root mean sq
39. s of the molecule respectively in a data format compatible with Protein Data Bank The file time d contains the time series of some quantities In our template we measure and store in this file the total energy eol the radius of gyration rgy by means of subroutine RGYR the number of helical beta sheet like residues nhel nbet and segments mhel mbet using subroutine HELIX and the number of hydrogen bonds mhb calculated through subroutine HBOND e Subroutine ANNEAL file anneal f This subroutine allows for optimization of protein conformations by means of sim ulated annealing When the logical parameter lrand is set to TRUE then the program will start from a random configuration Otherwise the annealing process will start from the current configuration as stored in the array vlvr In PARAM ETER statements the user has to set the initial and final temperatures tmax and tmin the number of Monte Carlo sweeps for simulation NSWP and equilibration negui and the number nmes of Monte Carlo sweeps between measurements Four output files are created in the same directory where the executable is running three of them contain the start start pdb the final final pdb and the global minimum configuration global pdb respectively the 4th file time d contains the time series of the simulation In the presented template we measure and store in this file the actual te
40. simulation is monitored by writing data into the file teme d after every 1000 sweeps The simulation shall start from a random configuration This leads to the following settings in the PARAMETER statements of anneal parameter lrand true parameter nequi 100 nswp 100000 nmes 1000 parameter tmax 1000 0 tmin 100 0 After compilation of SMMP with the make command and running the program from the sub directory EXAMPLES by the script cd smmp lt lt EXAMPLES enkefa seq EXAMPLES enkefa ann l 24 the output will contain the energy of the true start configuration energy after eguili bration the average acceptance rate of moves in the simulated annealing run the final configuration and its energy and the configuration with the lowest energy found in this run file with SEQUENCE EKAMPLES enkefa seg file with VARIABLES EXAMPLES enkefa ann redvar gt Met Enkephalin residue 2 Gly omg set 180 000 Fixed redvar gt Met Enkephalin residue 3 Gly omg set 180 000 Fixed redvar gt Met Enkephalin residue 4 Phe omg set 180 000 Fixed redvar gt Met Enkephalin residue 5 Met omg set 180 000 Fixed redvar gt Met Enkephalin residue 5 Met omt set 180 000 Fixed redvar gt Molecule Met Enkephalin 19 variable s remain unchanged energy of start configuration 0 34360E 08 Energy after equilibrisation 24 03751 acceptance rate 0 186481819 last energy 6 56133682 1 xi 173 7 ie Sr 106 4 Li KO 3
41. uare deviation rmsd between atom postions in the current configuration of molecule nml for a range of residues ir1 ir2 and a reference structure given by arrays of atom coordinates arf yrf zrf For each atom position in the current SMMP structure the array izat provides the index of the equivalent atom in the reference structure or yields a value of 0 if there is no equivalent By setting zs 0 the rmsd is calculated over all non hydrogen heavy atoms for is 1 for backbone atoms only and for isl 2 the rmsd is calculated only between C atoms The routine rmsdfun may only be called after an initial call of the subroutine rmsinit nml string If string smmp the reference configuration is a SMMP configuration otherwise it is read in from a PDB file which name given by string Subroutine ZIMMER Usage call zimmer nresi This subroutine analyzes the backbone dihedrals of a given conformation and char acterizes the state of each pair of 4 by its Zimmerman code The subroutine requires as input the number of residues nresi and returns the character string zimm with the Zimmerman code of the present configuration through a common block 17 7 How to Run SMMP SMMP does not include an interpretor of user defined commands The preparation of a simulation must be done in the MAIN module calling corresponding simulation sub routine s After changing of these modules SMMP
42. ughout the whole simulation process Spaces are not significant and are therefore ignored Empty COMMANDS as and empty lines or lines containing are ignored Missing fields are interpreted as for all 1 phi 180 Set phi of residue 1 to 180 degrees 1 phi 1804 Keep phi of residue 1 fixed to 180 degrees phi 180 Set phi of ALL residues to 180 degrees 180 Set all variables to 180 degrees Several consecutive residues or variables can be indicated by ZONES of indices Several NAMES can be indicated by wild card and are case sensitive 1 4 phi 180 Set phi of residues 1 2 3 and 4 to 180 deg 5 x 60 Set all xi angles of residue 5 to 60 deg Several NAMES or INDICES may be given in the same field when separated by Similarly several commands may be given on the same line and must be separated by phi psi 30 Set all phi amp psi to 30 deg phi 65 psi 45 Set all phi 65 all psi 45 Note that dihedral angles are defined slightly differently in SMMP than in standard ECEPP residue index in parenthesis 10 psi of the i th residue defined by N i 1 CA i 1 C i 1 N i omg of the i th residue defined by CA i 1 C i 1 N i CA i phi for the i th residue defined by C i 1 N i CA i C i except phi for the ist residue defined by H1 1 N 1 CA 1 C 1 H2 atom in the N terminal NH2 group is added via dihedral H
43. with an energy as low as possible This process of fitting a PDB structure into standard geometry is called regularization regul requires the PDB structure to be read into SMMP by setting zabin 0 in main With this option init_molecule calls the subroutines pdbread and pdbvars that also to measure the dihedral angles in the PDB structure Using these dihedral angles a first model of the molecule is built using standard bonding geometry Hence regul has to be called AFTER init_molecule nm has to be set to 1 in the present version of SMMP regul starts with a minimization of the initial structure using only the sum of squared distances between atom positions of the SMMP structure to the PDB structure as constraint energy After this initial step a list of bad atom contacts i e atoms with vdW energy of more than 2 kcal mol as calculated by cnteny and the root mean square deviation rmsd to the PDB structure is printed out In a second step the physical energy is minimized allowing only hydrogens to move and bad contacts and the rmsd are evaluated again A number of iterations follow where a composite energy as the weighted sum of physical and constraint energy is minimized In this iterations the weight of the constraint energy is successively lowered to zero and that of the physical energy raised to one At the end the dihedral angles of the final structure are printed out together with
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