[gmx-users] Development of .ITP or .TOP file for non-standard molecules

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 5 18:54:04 CEST 2007

Michelle Hyers wrote:
> Hey everyone,
> I am trying to setup a MD simulation of non-protein molecules (for
> example, C18H37Cl3Si)and I was wondering if there is an easy way to
> setup the .top or .itp files for the molecule. I was specifically
> wondering if information in the file, such as bonds, pairs, angles,etc.
> has to manually determined for each molecule or if there is a way to
> output the information from an existing file format such as from a
> standard chemical drawing program like ChemDraw or other graphical
> interface directly to the require gromacs file types. Any advice about
> this issue would be appreciated!
try x2top in 3.3.2, you will need to edti the file ffoplsaa.n2t in the 
share/gromacs/top directory.

> Thanks!
> Michelle H.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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