[gmx-users] Carbohydrate MD Simulation

Bruce D. Ray brucedray at yahoo.com
Sat Aug 1 17:31:12 CEST 2009

On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy <nancy5villa at 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
I hope one of these with careful selection of the force field will be helpful to you.


Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273

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