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DocumentsDate added
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VMD script for sorting/unsorting residueshot!
- 01.08.2006
- This is especially useful if you have run some simulations of a system using the -sort -shuffle options of grompp, and some others without the -sort option. You may either want to recover the original order for the resulting files, or convert the initial files to the New Order (TM). Grompp writes an index file that allows you to undo the shuffling, but gives no information on the reordering...
- Hits: 2491
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Updated OPLS-AA fileshot!
- 09.09.2005
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This version of OPLS will be in the next Gromacs version, but in the meantime you can download this file and unpack it in your topology directory. The changes are minor, but involve using 4.184 instead of 4.1868 for converting between kcal and kJ, and changing the atom order for some improper torsions.
Uploaded 09:33 August 06, 2003 by Erik Lindahl (lindahl@stanford.edu) - Hits: 2820
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trjconv with extended fitting hot!
- 09.09.2005
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when doing -fit, allows two index groups to be given: -ns then selects from the structure file and -n selects from the trajectory and controls the output. Output may be slightly different (<= 0.005 A) to the standard version.
Uploaded 14:39 December 22, 2002 by Graham Smith (smithgr@cancer.org.uk - Hits: 2715
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topolbuild1_2hot!
- 08.10.2008
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Topolbuild 1.2
Reads a Tripos .mol2 file with charges to generate something approximating gromacs .gro, .top, and .itp files from it based on selected force field parameters. Now includes some support for united atom force fields. Includes tables to support amber, gaff, glycam, and gmx type force fields. Requires that the .mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types. Includes capability of pruning dihedral angles to a possibly more reasonable set.
Revisions include:- Corrected improper dihedrals determination.
- Added gromacs united atoms force fields, along with some required atom type definition files and parameters files. Atom type definition files and parameter files are included for gmx43a1, gmx43a2, gmx43b1, gmx45a3, gmx53a5, and gmx53a6. Only the table for gmx53a6 has received any checking. All of these tables are incomplete and to be considered experimental. As with any automatic system for parameterization, careful examination and editing of the results is required to generate a well behaved final topology.
- Added glycam force fields option and ATOMTYPE_GLYCAM.DEF. The glycam option is experimental and may not give a correct result.
- Added option to prune excess dihedral angles.
- Added conversion of some ring planarity dihedral angles to be output in the topology as improper dihedral angles.
- Added an internal adjustment to correct for the problem of programs other than Sybyl generating larger charges than those from the standard Sybyl residue dictionary and charge generation methods.
- Altered topology outputs to allow for various types of bond, angle, and dihedral angle parameters.
- Made changes to antechamber data tables to correct for problems related to gromacs case insensitivity and for the absence of some atom type combinations in the force field parameters.
Special Processing Used for Gromacs Force Fields
Gromacs force fields have a limited set of atom types that are used in multiple chemical environments. This works quite well when one can use a residue types file to generate a topology. This presents problems when the goal is to determine the topology of an arbitrary molecule for which residue type information does not exist. Therefore, conversion to gromacs force fields requires double determination of atom types. A first determination of atom types is performed with a rich set of atom types derived from a combination of the gaff and amber atom type definitions. This assignment is used to determine force constants, bond lengths, angles, dihedral angles, and improper angles. A second determination of atom types is performed to assign the true gromacs atom types to match the atom types in the appropriate ffG####nb.itp from the gromacs distribution. A major problem of this double conversion is that for something found in a residue type file, topolbuild does not always select the exact same parameters as are found in the residue type file’s parameterization. However, tests so far give the same parameterization better than 95% of the time.
- Hits: 121
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topolbuildhot!
- 17.08.2007
- Builds a Gromacs topology from a Tripos .mol2 file and a force field selected from gaff, amber## (where ## is the two digit year), or Tripos (when available). Uses the files in the antechamber-1.27 dat directories dat/antechamber and dat/leap/parm to build gaff or amber## based topologies. Uses the TAFF* files in the directory pointed to by Tripos variable $TA_ASCTABLES to build Tripos force field based topologies. Has an option for renumbering of atoms and residues to decrease the amount of editing needed to add ligands to a system. Has an option to allow use of measured values for bond lengths and angles. Converts distance restraints in the .mol2 file to Gromacs distance restraints. Has potential expandability to other all atom force fields with addition of appropriate atom type definition files.
- Hits: 1225
