minCHARMM.pl - Revision history

Maciej at 13:47, 16 September 2016

2016-09-16T13:47:44Z

Maciej at 13:46, 16 September 2016

2016-09-16T13:46:04Z

Maciej at 13:37, 16 September 2016

2016-09-16T13:37:55Z

Maciej at 13:24, 16 September 2016

2016-09-16T13:24:07Z

Edit: /* Options */

2009-07-31T03:06:04Z

Options

Edit: /* Description */

2009-07-31T03:04:30Z

Description

Edit: /* Options */

2009-07-29T04:52:50Z

Options

Edit: /* Options */

2009-07-29T02:03:23Z

Options

Edit: /* Options */

2009-07-29T01:52:25Z

Options

Edit: /* Options */

2009-07-29T01:50:39Z

Options

@@ Line 33: / Line 33: @@
 <B>-cons</B> 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 id.
+Selection of the residues may require use of the chain or segment ids,
-Especially when the residues numbering is not continuous.
+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>,

@@ Line 32: / Line 32: @@
 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
-applied and corresponding force constants. By default all heavy atoms will be
+applied and corresponding force constants.
 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,

←Older revision		Revision as of 13:37, 16 September 2016
Line 110:		Line 110:

	<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>

@@ Line 90: / Line 90: @@
 ; -mol2 MOL2file : use speficied mol2 file to setup topology
 ; -crdout : write final structure in CRD format
 ; -l [ca|cb|cab|heavy] force self|refpdb min&#58;max[=...] : a restraint is applied to all specified atoms that are not given in the residue range
 ; -cons [ca|cb|cab|heavy] self|refpdb min&#58;max[_force][=...] : a harmonic restraint is applied to all specified atoms given in the residue range
-; -hmcm chainFile min&#58;max[_force][=...] : a harmonic center of mass restraint is applied to all specified atoms given in the residue range
+; -l [ca|cb|cab|heavy] force self|refpdb [chain|segment&#58;]min&#58;max[_force][=...] : a restraint is applied to all specified atoms that are not given in the residue range
-; -rmsd [ca|cb|cab|heavy] refpdb refval min&#58;max[_force][=...] : a rmsd-based restraint, calculated with respect to a reference structure, is applied to all specified atoms given in the residue range
+; -cons [ca|cb|cab|heavy] self|refpdb [chain|segment&#58;]min&#58;max[_force][=...] : a harmonic restraint is applied to all specified atoms given in the residue range
 ; -custom file[&#58;file] : reads in additional CHARMM commands via a custom file
 ; -log logFile : generates a log file

@@ Line 86: / Line 86: @@
 ; -help : usage information
-; -par : define CHARMM parameters (see [[CHARMM_Parameters | CHARMMparams]])
+; -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
+; -mol2 MOL2file : use speficied mol2 file to setup topology
-; -crdout :
+; -crdout : write final structure in CRD format
 ; -l [ca|cb|cab|heavy] force self|refpdb min&#58;max[=...] : a restraint is applied to all specified atoms that are not given in the residue range
 ; -cons [ca|cb|cab|heavy] self|refpdb min&#58;max[_force][=...] : a harmonic restraint is applied to all specified atoms given in the residue range

@@ Line 13: / Line 13: @@
 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>
 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 <B>-psf</B>.
-<BR><BR>
+<BR>
 Other command-line options are available to change the default protocol, introduce
 restraints and specify output files:<BR><BR>
@@ Line 23: / Line 25: @@
 list of all available parameters is given
 [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters here].
-<BR><BR>
+<BR>
 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
@@ Line 35: / Line 38: @@
 atom positions from this file are used instead of the initial coordinates from the
 input file.<BR>
 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.
@@ Line 45: / Line 49: @@
 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
 file from the MONSSTER program. This option <B>-hmcm</B> is available for use with
@@ Line 56: / Line 61: @@
 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.<BR><BR>
+does not allow the use of more than one reference file.<BR>
 For special applications that involve CHARMM commands that are not supported
 through the options of minCHARMM.pl it is possible to include arbitrary CHARMM
@@ Line 62: / Line 68: @@
 corresponding commands are executed after all the standard energy functions
 are setup but before the first minimization run.
-<BR><BR>
+<BR>
 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
 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>.
-<BR><BR>
+<BR>
 The location of the CHARMM binary and data directory are expected
 from the environment variables CHARMMEXEC and CHARMMDATA. Otherwise an attempt

@@ Line 78: / Line 78: @@
 ; -help : usage information
+; -par : define CHARMM parameters (see [[CHARMMparams]])
 == Examples ==