[gmx-users] Does Gromacs work on a molecule which is not protein

David van der Spoel spoel at xray.bmc.uu.se
Wed May 17 17:39:11 CEST 2006

Tanping Li wrote:
> Dear all,
> I plan to run solvate a small molecule using Gromacs.
> This small molecule is not a protein or DNA or RNA. So
> I meet the problem at the first step to run pdb2gmx,
> the wrong information says Gromacs can't recognize
> this molecule.
> Is there a way to assign charge to this small molecule
> and get a *.top file; could I use gromacs to run this
> unknown small molecule?

of course, you have to use other software and your editor to create the 
topology. you can also start with prodrg.

> Thank you very much for your suggestion. I have
> bothered by this for a while.
> Best
> Tanping
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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