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     43A1-S3.tar.gz
    The 43A1-S3 forcefield is an improved forcefield suited for molecular dynamics simulations of lipid bilayers systems. The forcefield has been parameterized in a progressive way, based on the reproduction of molecular volumes and heats of vaporization of small chemical species modelled for the fragments of lipids. This parameter set is validated by MD simulations that replicate experimental structures of bilayers including X-ray form factors, order parameters (J. Phys. Chem. B, 2009, 113, 2748–2763).
    		145.42 kB22:49, 4 Jan 2011schiuActions
     53a5.tar.gz
    The GROMOS 53a5 force field (see J. Comput. Chem. 2004 vol 25 pag 1656) in gromacs format. These files were used to calculate the solvation free-energy for amino-acid side chains and in protein simulations. Please check them before using them in particular if you simulate not-protein systems. Uploaded 13:18 August 30, 2004 by Alessandra Villa (villa at theochem.uni-frankfurt.de)
    		58.45 kB10:13, 23 May 2009rossenActions
     53a6.tar.gz
    The GROMOS 53a6 force field (see J. Comput. Chem. 2004 vol 25 pag 1656) in gromacs format. These files were used to calculate the solvation free-energy for amino-acid side chains and in protein simulations. Please check them before using them in particular if you simulate not-protein systems. Uploaded 13:19 August 30, 2004 by Alessandra Villa (villa at theochem.uni-frankfurt.de)
    		58.44 kB10:10, 23 May 2009rossenActions
     56a_CARBO4GROMACS.rar
    The GROMOS 56a_Carbo [J Comput Chem. 2011; 32 (6): 998-1032] force field in GROMACS format. The files correspond to four types of building blocks based on the beta-D-glucose molecule.
    		54.17 kB11:42, 7 May 2013wojtekp?Actions
     amber99sb_parmbsc0.ff.tgz
    Amber99sb force field with the ParmBSC0 nucleic acid parameters added (GROMACS 4.5.x format). If you use these files please cite: http://dx.doi.org/10.1016/j.bpj.2012.08.012 in addition to the original force field publications.
    		30.79 kB10:05, 5 Sep 2012TomPiggotActions
    CGenffRevB.tar.gz
    Added sample solvent *.itp files that can be used with sample.top
    		449.42 kB15:09, 1 Nov 2011fabian.casteblanco?Actions
     charmm22star.ff.tgz
    CHARMM22* force field. Backbone CMAP correction replaced with new torsions (excluding G, P), new partial charges for R, D, and E side chains, and new side chain torsions for D. Adapted from CHARMM27 parameters included with Gromacs 4.5.3. From Piana, S., et al. Biophys J. 2001. 100. L47-L49.
    		590 kB14:11, 9 Jul 2012ktd3?Actions
     charmm36.ff_4.5.4_ref.tgz
    GROMACS 4.5.4 version of the CHARMM36 force field files. These updated CHARMM lipids allow the all-atom simulations of membrane and membrane-protein systems without the use of surface tension. Check out the forcefield.doc for more information regarding these files
    		71.65 kB15:42, 25 Sep 2012TomPiggotActions
     chcl3_box.tgz.tgz
    atom types are named opls_X, where X is the OPLS number. Uploaded 10:26 February 12, 2004 by Anonymous (Not e-mail)
    		43.25 kB10:09, 23 May 2009rossenActions
     ff03-star.tgz
    ff03* force field, JPCB v113, p9004, 2009. Modification of amber ff03 to match helix-coil data.
    		31.63 kB11:55, 8 Feb 2011rbb24Actions
     ff03w.tgz
    ff03w force field (Amber03 adapted for use with Tip4p/2005 water model)
    		73.17 kB10:28, 18 Aug 2012rbb24Actions
     ff99sb-star-ildn.tgz
    Combination of DE-shaw ILDN modifications with ff99SB* force field [JPCB v113, p9004, 2009. Modification of amber ff99SB to match helix-coil data].
    		34.06 kB11:55, 8 Feb 2011rbb24Actions
     ff99sb-star.tgz
    ff99SB* force field, JPCB v113, p9004, 2009. Modification of amber ff99SB to match helix-coil data.
    		30.41 kB11:55, 8 Feb 2011rbb24Actions
     ffamber_v1.0-doc.tar.gz
    Several AMBER protein and nucleic acid force fields are available with complete documentation. Please see the ffamber website at http://folding.stanford.edu/ffamber/ for details, as our ports and accompanying documentation will be updated there until integration into future GROMACS distributions. Uploaded 16:55 June 30, 2005 by Eric J. Sorin (esorin at stanford.edu)
    		6.04 MB10:13, 23 May 2009rossenActions
     ffG43a1p.tar.gz
    G43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine), and PTR (phosphotyrosine) (all PO4^{2-} forms), and SEPH, TPOH, PTRH (PO4H^{-} forms). The charges and vdw parameters come from Hansson, Nordlund and Aqvist jmb 265 118-27 1997. They worked mostly with gromos 87 but I generally use gromos 96 so I\'ve made the files in that format (there seem to be no differences in the amino acid charges between 87 and 96). Hansson et al don\'t report bond angle or dihedral parameters, and I don\'t know how to do QM calculations, so I\'ve used the standard forms from the *bon.itp file. For the dihedrals, I\'ve used the 3-fold gd_11. Because of their symmetry, the PO4^{2-} forms at least cannot have the 2-fold + 3-fold symmetry used in the gmx DNA bases. The OP-X LJ-14 parameters are the same as for OA. I\'ve checked that I can build simple 1-molecule topologies and tprs for the PO4H forms, and for the PO4 forms have done 100 ps solvated MD of the isolated am acs and the am acs in proteins (1f1w, 1fu0, 1qmz). I\'ve checked water-phosphate rdfs and parameters in gmxdumped tprs. Uploaded 16:08 May 15, 2002 by Graham Smith (smithgr@cancer.org.uk)
    		46.86 kB10:13, 23 May 2009rossenActions
     ffG43a2x.tgz
    The normal version of the GROMOS96 force field results in bad area/lipid and volume/lipid for most lipid membranes. This version of the force field has been extended with new LCH2 and LCH2 united atom types which reproduce the experimental properties of both long hydrocarbons and membranes. Uploaded 17:58 June 08, 2001 by Erik Lindahl (erik@theophys.kth.se)
    		44.23 kB10:10, 23 May 2009rossenActions
     ffG45a3.tar.gz
    This force field was created using GROMOS96 43a1 as base and the parameters given by the article An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. Journal of Computational Chemistry 22 (11), August 2001,1205-1218 by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren. The initial work was performed by christoph riplinger and was later corrected and completed by myself and alessandra villa (villa at theochem.uni-frankfurt.de) who kindly provided the original gromos format file of this force field. Uploaded 17:17 July 19, 2004 by Jaime arce (arce at ibsm.cnrs-mrs.fr)
    		46.38 kB10:10, 23 May 2009rossenActions
     ffgmx_lipids.tar.gz
    These are the params from lipid.itp incorporated into the ffgmx*.itp files, as the newer gromacs versions require it. Copy these modified files into the .../gmx/share/top directory or in your current working dir. Uploaded 10:02 January 14, 2003 by Bert de Groot (bgroot@gwdg.de)
    		19.91 kB10:09, 23 May 2009rossenActions
     ffoplsaanr.tar.gz
    We added DNA/RNA records to OPLS forcefield. Here you can download version with RESP charges (from Amber). We tested this one more or less. Results you can found at: http://rnp-group.genebee.msu.su/3d/oplsa_ff.html. At that page you can find forcefield with another charges, but this one is not tested. Recently we added 3` and 5` end residues. Scripts that fix pdb to make them compatible with pdb2gmx are here: fixpdb_dna and fixpdb_rna This scripts also works with NA-protein complexes. Uploaded 19:09 March 08, 2005 by Andrey Golovin and Nikita Polyakov (golovin at genebee.msu.su)
    		61.27 kB10:09, 23 May 2009rossenActions
     gromos43a1p-4.5.1.tgz
    Force field files for Gromos96 43a1p, re-formatted to be compatible with newer versions of Gromacs (4.0 and beyond). This particular archive organizes the files such that they are compatible with version 4.5.x. Please note that the parameters are unmodified relative to what was contributed by Graham Smith. I take no credit for these parameters; I just made the files compatible with the current version of Gromacs.
    		47.13 kB21:49, 25 Oct 2010JLemkul?Actions
     gromos56a6_withAZE_support.zip
    This is a modified GROMOS 53a6 forcefield that supports non-natural Aze (azetidine-2-carboxylic acid) amino acid that is similar to Proline, except that it has a 4-atom instead of a 5-atom ring. Aze occurs naturally in plants and was shown to have toxic effects in mammalian cells possibly due to its hability to be misincorporated into growing polypeptide chains instead of Proline. We found that Aze has greater propensity to adopt a cis-peptide bond conformation compared to Proline . To install this modified Gromos56a6 forcefield simply unzip the archive in the forcefield folder. Reference: Bessonov K, Vassall KA, Harauz G. Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations. J Mol Graph Model. 2013 Feb; 39:118-25
    		89.16 kB20:40, 24 Feb 2013kbessonov?Actions
     lipid_forcefield.ff.tar.gz
    All-atomisic force field for phosphatidylcholine lipids. Contains parameters for fully saturated chains, soon unsaturated chains and other head groups will be included. Compatible with the AMBER force fields for proteins. This set of parameters reproduces a lot of experimental data such as area per lipid and thickness(es) but most importantly scattering form factors con order parameters are reproduced. Ref: J. Phys. Chem. B, DOI: 10.1021/jp212503e
    		31.36 kB16:28, 4 Mar 2012joakim?Actions
    Page last modified 13:32, 19 May 2009 by lindahl