[gmx-users] Prodrg

David spoel at xray.bmc.uu.se
Fri Oct 14 22:55:42 CEST 2005

On Fri, 2005-10-14 at 12:32 -0700, Rodrigo Reston wrote:
> Just expanding my previous e-mail:
> Hi. I used Prodrg server to create the coordinates
> and topology for a molecule. None of the .top files
> available at the server, after I make the run,
> work. [ I cannot create a .top using x2top because
Please be more specific on what kind of molecule, and what you mean with
does not work.

> there's a problem in the .gro file - it always
> complains about the FF not having the type for some
> atom in the structure that's forming illegal bonds -
> even if I change the molecule just a bit. I have no
> idea what to do with the .itp file. ] And I cannot
> generate a .top file using the .pdb file through
> pdb2gmx because Gromacs does not recognize the "DRG"
> residue!
> I sorry, I thought I could be more specific but I
> can't. 
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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://xray.bmc.uu.se/~spoel

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