[gmx-users] grompp problem

[David van der Spoel]

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.
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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