[gmx-users] grompp problem

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 15 21:55:31 CET 2007


Now before anything else..., do you need a CB to be defined? Doesn't
one of the atom types present suffice? There's tyrosine in most force
field already, you know, and these 'CB' atoms are merely part of the


On 3/15/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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