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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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