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Downloads
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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: 2342
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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: 2665
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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: 2563
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topolbuild1_1_2hot!
- 10.07.2008
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Reads a Tripos .mol2 file with charges to generate something approximating a gromacs .gro and .itp from it based on an all-atoms force field. Does not work at this time with a united atoms force field. Only amber and gaff force fields have the necessary tables at this time. Requires that the .mol2 file have syntactically correct Tripos atom types and absolutely will not work with other input atom types.
Further revisions both to improve the topologies produced and to be compatible with the new versions of the antechamber tables released with AmberTools 1.0.
- Changed maximum atom types allowed to permit use of the new version of ATOMTYPE_GFF.DEF distributed with AmberTools 1.0.
- Improved determination of improper dihedrals.
- Corrected atom type determination to set and to check for plain type AB bonds.
- Made cosmetic corrections to log file output.
- Included a gaff.dat file modified from the one distributed with AmberTools 1.0 to add atom type cz entries for mass and polarizability, for improper dihedrals, and for van Der Waals interactions.
- Replaced the ATOMTYPE_GFF.DEF file with one derived from the ATOMTYPE_GFF.DEF distributed with AmberTools 1.0.
- Hits: 111
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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: 1074
