[gmx-users] Prodrg

David spoel at xray.bmc.uu.se
Sat Oct 15 10:39:25 CEST 2005

On Fri, 2005-10-14 at 15:08 -0700, Rodrigo Reston wrote:
> Ok. The molecule I'm trying to get the coordinates and
> topology for is a naphthalene derivative to which an
> amino or nitro group may be bonded in the position 4 ,
> or not. So, I'd like to have 3 computer models with
> which I could work in molecular dynamics simulations.
> None of the .top files available in the Prodrg server
> worked - first, I should have asked what was I
> supposed to do with the topology file .itp found in
> the Docking / MD simulations for Gromacs.

You'll find this information in ch. 5 of the manual.

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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