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Difference between revisions of "minCHARMM.pl"
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is carried out with the CHARMM22 protein force field in vacuum (constant dielectric | 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.<BR> | of 1.0) with a 14.0 A cutoff for non-bonded interactions.<BR> | ||
| + | |||
Normally a PDB file containing the protein structure is expected as the last | Normally a PDB file containing the protein structure is expected as the last | ||
command line argument or through standard input. Alternatively, it is also | 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 | possible to use CHARMM PSF and CRD files instead of a PDB file with the | ||
option <B>-psf</B>. | option <B>-psf</B>. | ||
| − | <BR> | + | <BR> |
| + | |||
Other command-line options are available to change the default protocol, introduce | Other command-line options are available to change the default protocol, introduce | ||
restraints and specify output files:<BR><BR> | restraints and specify output files:<BR><BR> | ||
Minimization parameters can be set with <B>-par</B> followed by key=value pairs. A | Minimization parameters can be set with <B>-par</B> followed by key=value pairs. A | ||
list of all available parameters is given | list of all available parameters is given | ||
| − | + | [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters here]. | |
| − | <BR> | + | <BR> |
| + | |||
Different types of restraints may be specified to keep parts of the structure | 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 | near their initial positions or near coordinates from a reference file. This is | ||
| Line 29: | Line 32: | ||
Atom-based restraints are specified with <B>-cons</B> or <B>-l</B>. | Atom-based restraints are specified with <B>-cons</B> or <B>-l</B>. | ||
<B>-cons</B> requires a list of residue ranges where the restraints should be | <B>-cons</B> requires a list of residue ranges where the restraints should be | ||
| − | applied and corresponding force constants. By default all heavy atoms will 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 <font color=#508060>ca</font>, | restrained to their initial positions. The keywords <font color=#508060>ca</font>, | ||
<font color=#508060>cb</font>, or <font color=#508060>cab</font> can be specified to select only C-alpha, C-beta, | <font color=#508060>cb</font>, or <font color=#508060>cab</font> can be specified to select only C-alpha, C-beta, | ||
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atom positions from this file are used instead of the initial coordinates from the | atom positions from this file are used instead of the initial coordinates from the | ||
input file.<BR> | input file.<BR> | ||
| + | |||
In loop modeling it is more convenient to specify the residues in the | 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. | loop rather than the residues outside the loop for which restraints would be requested. | ||
| Line 44: | Line 51: | ||
increasing force constants from the beginning and ends of the loop regions up to | 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 | the specified force constant in a similar fashion as the force constants generated by | ||
| − | + | [[genrestr.pl]] for lattice simulations.<BR> | |
| + | |||
Restraints can also be applied to side chain centers of mass based on a lattice chain | Restraints can also be applied to side chain centers of mass based on a lattice chain | ||
file from the MONSSTER program. This option <B>-hmcm</B> is available for use with | file from the MONSSTER program. This option <B>-hmcm</B> is available for use with | ||
| Line 56: | Line 64: | ||
of the same residues to coordinates from a reference file but not C-alpha | of the same residues to coordinates from a reference file but not C-alpha | ||
restraints from both initial positions and reference coordinates. CHARMM also | restraints from both initial positions and reference coordinates. CHARMM also | ||
| − | does not allow the use of more than one reference file.<BR> | + | does not allow the use of more than one reference file.<BR> |
| + | |||
For special applications that involve CHARMM commands that are not supported | For special applications that involve CHARMM commands that are not supported | ||
through the options of minCHARMM.pl it is possible to include arbitrary CHARMM | through the options of minCHARMM.pl it is possible to include arbitrary CHARMM | ||
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corresponding commands are executed after all the standard energy functions | corresponding commands are executed after all the standard energy functions | ||
are setup but before the first minimization run. | are setup but before the first minimization run. | ||
| − | <BR> | + | <BR> |
| + | |||
The final structure after minimization is written to standard output. | The final structure after minimization is written to standard output. | ||
The options <B>-log</B> and <B>-elog</B> are available to save the complete | The options <B>-log</B> and <B>-elog</B> are available to save the complete | ||
output from CHARMM or only the energy values at each printed minimization | output from CHARMM or only the energy values at each printed minimization | ||
step, respectively. Commands sent to CHARMM are saved to a file with <B>-cmd</B>. | step, respectively. Commands sent to CHARMM are saved to a file with <B>-cmd</B>. | ||
| − | <BR> | + | <BR> |
| + | |||
The location of the CHARMM binary and data directory are expected | The location of the CHARMM binary and data directory are expected | ||
from the environment variables CHARMMEXEC and CHARMMDATA. Otherwise an attempt | 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 | is made to locate the CHARMM binary from the search path and deduce the data | ||
directory from the binary location.<BR><BR> | directory from the binary location.<BR><BR> | ||
| − | A similar script | + | A similar script [[minAmber.pl]] is available for minimizations |
using the Amber molecular mechanics package. | using the Amber molecular mechanics package. | ||
| Line 78: | Line 89: | ||
; -help : usage information | ; -help : usage information | ||
| + | ; -par key=value[,...] : define CHARMM parameters (see [[CHARMM_Parameters | 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 == | == Examples == | ||
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<mmtsbToolExample cmd="minCHARMM.pl" set="/apps/mmtsb/bench/minCHARMM.pl-test/test4"></mmtsbToolExample> | <mmtsbToolExample cmd="minCHARMM.pl" set="/apps/mmtsb/bench/minCHARMM.pl-test/test4"></mmtsbToolExample> | ||
| + | |||
| + | <mmtsbToolExample cmd="minCHARMM.pl" set="/apps/mmtsb/bench/minCHARMM.pl-test/test5"></mmtsbToolExample> | ||
Latest revision as of 13:47, 16 September 2016
Usage
usage: minCHARMM.pl [options] [PDBfile] options: [-par CHARMMparams] [-psf PSFfile CRDfile] [-mol2 MOL2file] [-crdout] [-nochain] [-splitseg] [-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]
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 ...