[gmx-users] Prodrg

David spoel at xray.bmc.uu.se
Fri Oct 14 08:21:55 CEST 2005

On Thu, 2005-10-13 at 15:14 -0700, Rodrigo Reston wrote:
> 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

please be more specific, and also read ch. 5 of the manual.

> cannot create a .top using x2top because there's a
> problem in the .gro file. I don't know how to use the
> .itp file. And I cannot generate a .top file using the
> .pdb file because Gromacs does not recognize the "DRG"
> residue!
> So, I would very much like to know HOW to solve the
> "DRG" residue problem and HOW I was supposed to use
> the .itp file. Any other suggestions will be very much
> appreciated too!
> Thanks!
> Rodrigo S. Reston, BSc.
> UFMG, Brazil.
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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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