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.

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