[gmx-users] Problems with GROMPP

Jens Pohl Pohl.Jens at web.de
Tue Jan 15 18:55:01 CET 2008

> >> I'd echo Justin's request for your *actual* commands. Computers are very
> >> literal, and we'd rather have your original commands than something
> >> that's clearly been filtered through your head. If the above reflects
> >> your actual use of wildcards on the command line, that sounds like a
> >> possible source of problems.
> >>
> >> Mark
> >
> > Of cause I didn't use those wildcards, but instead of the * I used   
> > the name of the file xxx, so that for pdb2gmx it reads
> > ~$: ../bin/pdb2gmx -f ./xxx.pdb -o ./out -p ./out -q ./out.pdb -n   
> > ./out -i ./out
> >
> > In the meantime I've redone it several times and finally got some   
> > input files for grompp and mdrun (next problems ahead, but I try to   
> > solve them ;-)  )
> >
> > Jens
> Hi Jens,
> When some people have already donated their time to assist you and  
> then you figure it out on your own, I suggest that you consider  
> posting a description of the actual problem and the solution that you  
> found. It will enhance your chances of getting a timely reply to your  
> next problem.
> Chris.

Hi Chris,

I'm really greatful for the help, and as I wrote I've just redone the things I did before... same input-files, same options. I don't know why it worked the last time I did it. All I know is that I had the problem with genbox which truncated the protein at different sites (in the xxx.gro file) and which then resulted in the problems with grompp because the xxx.top wasn't affected.


Unbegrenzter Speicherplatz für Ihr E-Mail Postfach? Jetzt aktivieren!

More information about the gromacs.org_gmx-users mailing list