MMTSB
Tool Set Documentation

minCHARMM.pl

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Usage

usage:   minCHARMM.pl [options] [PDBfile]
options: [-par CHARMMparams]
         [-psf PSFfile CRDfile]
         [-mol2 MOL2file]
         [-crdout]
         [-nochain]
         [-l [ca|cb|cab|heavy] force self|refpdb min:max[=...]]
         [-cons [ca|cb|cab|heavy] self|refpdb min:max[_force][=...]]
         [-hmcm chainFile min:max[_force][=...]]
         [-rmsd [ca|cb|cab|heavy|cap|cabp] refpdb refval min:max[_force][=...]]
         [-custom file[:file]]
         [-comp PDBfile]
         [-log logFile] [-elog energyLogFile]
         [-cmd logFile]
Show source


Description

This script is used to minimize a protein structure with CHARMM. Without any options a 50-step steepest descent minimization is followed by the more aggressive adopted-basis Newton-Raphson (ABNR) minimization algorithm over 500 steps or until the energy decrease between steps becomes less than 1.0E-5 kcal/mol. With the default protocol the minimization is carried out with the CHARMM22 protein force field in vacuum (constant dielectric of 1.0) with a 14.0 A cutoff for non-bonded interactions.

Normally a PDB file containing the protein structure is expected as the last command line argument or through standard input. Alternatively, it is also possible to use CHARMM PSF and CRD files instead of a PDB file with the option -psf.

Other command-line options are available to change the default protocol, introduce restraints and specify output files:

Minimization parameters can be set with -par followed by key=value pairs. A list of all available parameters is given here.

Different types of restraints may be specified to keep parts of the structure near their initial positions or near coordinates from a reference file. This is useful for modeling of fragments or loops in otherwise known structure templates. Atom-based restraints are specified with -cons or -l. -cons requires a list of residue ranges where the restraints should be applied and corresponding force constants. Selection of the residues may require use of the chain or segment ids, especially when the residues numbering is not continuous. By default all heavy atoms from the selection will be restrained to their initial positions. The keywords ca, cb, or cab can be specified to select only C-alpha, C-beta, or C-alpha/C-beta restraints, respectively. If a file name is given, the reference atom positions from this file are used instead of the initial coordinates from the input file.

In loop modeling it is more convenient to specify the residues in the loop rather than the residues outside the loop for which restraints would be requested. The option -l is available to specify a range of residues that are kept flexible, while restraints are generated implicitly for all other residues outside the given residue range(s). The syntax is otherwise similar to -cons. However, only a single force constant can be supplied as an extra argument. The restraints are generated with continuously increasing force constants from the beginning and ends of the loop regions up to the specified force constant in a similar fashion as the force constants generated by genrestr.pl for lattice simulations.

Restraints can also be applied to side chain centers of mass based on a lattice chain file from the MONSSTER program. This option -hmcm is available for use with CHARMM versions c28a2 or newer and requires the name of a corresponding lattice chain file and a list of ranges for residues for which the side chain centers should be restrained in this way.
It is possible to combine different restraints in a limited fashion. Side chain center based restraints are independent from atom-based restraints but CHARMM does not allow more than one restraint per atom. Thus it is possible, e.g., to restrain C-alpha coordinates to their initial positions and C-beta positions of the same residues to coordinates from a reference file but not C-alpha restraints from both initial positions and reference coordinates. CHARMM also does not allow the use of more than one reference file.

For special applications that involve CHARMM commands that are not supported through the options of minCHARMM.pl it is possible to include arbitrary CHARMM commands from an external file given with -custom. In this case the corresponding commands are executed after all the standard energy functions are setup but before the first minimization run.

The final structure after minimization is written to standard output. The options -log and -elog are available to save the complete output from CHARMM or only the energy values at each printed minimization step, respectively. Commands sent to CHARMM are saved to a file with -cmd.

The location of the CHARMM binary and data directory are expected from the environment variables CHARMMEXEC and CHARMMDATA. Otherwise an attempt is made to locate the CHARMM binary from the search path and deduce the data directory from the binary location.

A similar script minAmber.pl is available for minimizations using the Amber molecular mechanics package.

Options

-help 
usage information
-par key=value[,...] 
define CHARMM parameters (see CHARMMparams)
-psf PSFfile CRDfile 
use specified protein structure file (PSF) and coordinate file (CRD) (see genPSF.pl)
-mol2 MOL2file 
use speficied mol2 file to setup topology
-crdout 
write final structure in CRD format


-l [ca|cb|cab|heavy] force self|refpdb [chain|segment:]min:max[_force][=...] 
a restraint is applied to all specified atoms that are not given in the residue range
-cons [ca|cb|cab|heavy] self|refpdb [chain|segment:]min:max[_force][=...] 
a harmonic restraint is applied to all specified atoms given in the residue range
-hmcm chainFile [chain|segment:]min:max[_force][=...] 
a harmonic center of mass restraint is applied to all specified atoms given in the residue range
-rmsd [ca|cb|cab|heavy] refpdb refval [chain|segment:]min:max[_force][=...] 
a rmsd-based restraint, calculated with respect to a reference structure, is applied to all specified atoms given in the residue range
-custom file[:file] 
reads in additional CHARMM commands via a custom file
-log logFile 
generates a log file
-elog energyLogFile 
generates an energy log file
-cmd logFile 
generates a CHARMM input file

Examples

minCHARMM.pl 1vii.exp.pdb
performs a minimization in vacuum over 500 steps and writes the minimized structure to standard output

ATOM      1  N   MET     1       3.120  -9.864  -2.124  1.00  0.00      PRO0
ATOM      2  HT1 MET     1       3.940  -9.320  -1.706  1.00  0.00      PRO0
ATOM      3  HT2 MET     1       3.430 -10.213  -3.048  1.00  0.00      PRO0
ATOM      4  HT3 MET     1       2.865 -10.642  -1.486  1.00  0.00      PRO0
ATOM      5  CA  MET     1       1.992  -8.909  -2.263  1.00  0.00      PRO0
ATOM      6  HA  MET     1       2.363  -7.932  -1.986  1.00  0.00      PRO0
ATOM      7  CB  MET     1       1.468  -8.885  -3.727  1.00  0.00      PRO0
ATOM      8  HB1 MET     1       0.677  -8.103  -3.797  1.00  0.00      PRO0
ATOM      9  HB2 MET     1       0.977  -9.855  -3.963  1.00  0.00      PRO0
ATOM     10  CG  MET     1       2.535  -8.566  -4.798  1.00  0.00      PRO0

...


minCHARMM.pl -par gb,minsteps=300,minetol=1E-3,nocut -log charmm.log -elog ener.log 1vii.exp.pdb
performs minimization of the given PDB structure with Generalize Born-type implicit solvent over 300 steps or until an energy tolerance of 0.001 is reached. Also, effectively no cutoffs are used for non-bonded interactions. In addition to the minimized structure written to standard output, CHARMM output is written to charmm.log and a log of relevant energy terms, extracted from the CHARMM output, is written to ener.log.

ATOM      1  N   MET     1       1.131  -9.978  -4.054  1.00  0.00      PRO0
ATOM      2  HT1 MET     1       1.908 -10.386  -3.483  1.00  0.00      PRO0
ATOM      3  HT2 MET     1       1.536  -9.743  -4.980  1.00  0.00      PRO0
ATOM      4  HT3 MET     1       0.422 -10.741  -4.176  1.00  0.00      PRO0
ATOM      5  CA  MET     1       0.551  -8.779  -3.382  1.00  0.00      PRO0
ATOM      6  HA  MET     1       1.361  -8.083  -3.215  1.00  0.00      PRO0
ATOM      7  CB  MET     1      -0.564  -8.113  -4.242  1.00  0.00      PRO0
ATOM      8  HB1 MET     1      -0.945  -7.222  -3.691  1.00  0.00      PRO0
ATOM      9  HB2 MET     1      -1.425  -8.810  -4.347  1.00  0.00      PRO0
ATOM     10  CG  MET     1      -0.150  -7.607  -5.639  1.00  0.00      PRO0

...


minCHARMM.pl -par minsteps=300,sdsteps=20,param=19,dielec=rdie,epsilon=4.0 -cons ca self 1:36_0.5 -elog ener.log 1vii.exp.pdb
performs a vacuum minimization of the given PDB structure over 300 steps with 20 steps of initial steepest descent minimization. A distance dependent dielectric with epsilon=4 and the CHARMM19 force field are used. During the minimization C-alpha atoms of all residues (1 through 36) are restrained to their initial position with a force constant of 0.5 kcal/mol. The energies during the minimization run are written to ener.log.

ATOM      1  HT1 MET     1       0.880 -10.728  -3.979  1.00  0.00      PRO0
ATOM      2  HT2 MET     1       2.156 -10.010  -3.127  1.00  0.00      PRO0
ATOM      3  N   MET     1       1.437  -9.857  -3.864  1.00  0.00      PRO0
ATOM      4  HT3 MET     1       1.899  -9.610  -4.761  1.00  0.00      PRO0
ATOM      5  CA  MET     1       0.549  -8.789  -3.447  1.00  0.00      PRO0
ATOM      6  CB  MET     1      -0.497  -8.497  -4.518  1.00  0.00      PRO0
ATOM      7  CG  MET     1       0.077  -7.923  -5.806  1.00  0.00      PRO0
ATOM      8  SD  MET     1      -1.199  -7.607  -7.050  1.00  0.00      PRO0
ATOM      9  CE  MET     1      -1.606  -5.934  -6.639  1.00  0.00      PRO0
ATOM     10  C   MET     1      -0.154  -9.158  -2.155  1.00  0.00      PRO0

...


minCHARMM.pl -par gb,minsteps=1000,cuton=20,cutoff=22,cutnb=25 -l ca 1.5 1vii.exp.pdb 10:21 -elog ener.log 1vii.rebuilt.10:21.pdb
minimizes the structure from the input PDB file with Generalized Born implicit solvent using an interaction cutoff of 22, switching function onset of 20 A and a cutoff for the non-bonded list generation of 25 A. C-alpha atoms outside of residues 10 through 21 are restrained to the position in the reference PDB structure 1vii.exp.pdb. This example shows typical usage for fragment modeling where part of the protein structure is modeled against a fixed template structure.

ATOM      1  N   MET     1       1.232 -10.136  -4.152  1.00  0.00      PRO0
ATOM      2  HT1 MET     1       2.001 -10.528  -3.552  1.00  0.00      PRO0
ATOM      3  HT2 MET     1       1.658  -9.945  -5.081  1.00  0.00      PRO0
ATOM      4  HT3 MET     1       0.520 -10.897  -4.254  1.00  0.00      PRO0
ATOM      5  CA  MET     1       0.645  -8.898  -3.564  1.00  0.00      PRO0
ATOM      6  HA  MET     1       1.454  -8.188  -3.467  1.00  0.00      PRO0
ATOM      7  CB  MET     1      -0.462  -8.290  -4.480  1.00  0.00      PRO0
ATOM      8  HB1 MET     1      -0.791  -7.322  -4.031  1.00  0.00      PRO0
ATOM      9  HB2 MET     1      -1.351  -8.958  -4.492  1.00  0.00      PRO0
ATOM     10  CG  MET     1      -0.051  -7.967  -5.932  1.00  0.00      PRO0

...


minCHARMM.pl -par minsteps=1000 -cons ca self PRO0:2:10_5.0 1vii.exp.pdb
performs a minimization in vacuum over 1000 steps and writes the minimized structure to standard output. During the minimization, C-alpha coordinates from residues 2 to 10 in the PRO0 segment are restrained to the initial position with a force constant of 5 kcal/mol.

ATOM      1  N   MET 0   1       1.667 -10.285  -1.924  1.00  0.00      PRO0
ATOM      2  HT1 MET 0   1       2.659 -10.075  -1.585  1.00  0.00      PRO0
ATOM      3  HT2 MET 0   1       1.670 -11.130  -2.518  1.00  0.00      PRO0
ATOM      4  HT3 MET 0   1       1.077 -10.410  -1.077  1.00  0.00      PRO0
ATOM      5  CA  MET 0   1       1.290  -9.045  -2.675  1.00  0.00      PRO0
ATOM      6  HA  MET 0   1       2.040  -8.294  -2.458  1.00  0.00      PRO0
ATOM      7  CB  MET 0   1       1.288  -9.338  -4.203  1.00  0.00      PRO0
ATOM      8  HB1 MET 0   1       0.393  -9.936  -4.480  1.00  0.00      PRO0
ATOM      9  HB2 MET 0   1       2.191  -9.945  -4.455  1.00  0.00      PRO0
ATOM     10  CG  MET 0   1       1.377  -8.057  -5.067  1.00  0.00      PRO0

...