[gmx-users] question about pdb2gmx

Justin Lemkul jalemkul at vt.edu
Thu Jul 19 12:19:57 CEST 2012

On 7/19/12 6:17 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> thank you for your answer.
> I already tried the -ss command but nothing happens. The program just
> writes the topology file but it does not ask me anything. My command was:
> pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff amber03
> is there something wrong with this command?

No, it's fine.  How many cysteines are in the structure?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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