On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <nancy5vi...@gmail.com> wrote: > If it necessary to manually create force field parameters for each molecule, then how can one run a > simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for > which there are no existing force fields? > > Do you know of any other MD software package that is capable of running simulations on > arbitrary molecules without having to "piece together" a force field for each molecule?
Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at <http://labmm.iq.ufrj.br/mktop/>, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at <http://code.google.com/p/acpypi/>. I hope one of these with careful selection of the force field will be helpful to you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273
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