[gmx-users] grompp problem

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 15 21:52:18 CET 2007

Tom Lenaerts wrote:
>> Not only in atp, but also in bon and nb. nb is a bit easy, only LJ 
>> parameters. But for bon, you need to specify any bonded, angle, dihedral 
>> interaction that CB and CR61 have in your molecule.
> The structure of these files is completely unclear to me.  I also didn't find any explanation of the gromacs website.  Is there a online explanation of the format and how new entries can be added?
> I retrieved all information on PTR from the PRODRG server.  Isn't there some way to directly copy and paste this information in the confuguration files?
> Below the PTR info obtained from PRODRG
it is in the manual, chapter 5.

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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