[gmx-users] pdb2gmx not recognizing disulfides

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 2 16:07:29 CEST 2007

Russell Green wrote:
> Hmm...well the thing is, I just need a .tpr file (which I was getting 
> with pdb2gmx followed by grompp) so I can convert an amber pdb 
> trajectory to xtc format. The simulation is already complete, I'm just 
> converting it, but of course the atoms from the tpr need to match those 
> of the trajectory. So should I still be doing something different other 
> than my idea to change the residue names of the .itp files, as mentioned 
> previously? Sorry for some of my ignorance, I'm still new with much of 
> this. Thanks for all the suggestions and input!
> Thanks,
> Russell Green
for this purpose you could also use a pdb file.

David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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