[gmx-users] Carbohydrate MD Simulation

[Bruce D. Ray]

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
<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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