On 8/17/12 1:33 PM, Shima Arasteh wrote:
Hi,
The .pdb file either should be dowloaded from RCSB website or you need to
construct the structure by a software such as hyperchem and save the structure
in .pdb format, so you are not supposed to get .pdb output through pdb2gmx
command.
The output configuration produced by pdb2gmx can be any number of formats that
the user chooses. The .gro file format is default, but one can obtain .pdb,
.g96, etc. Gromacs programs accept and use numerous file formats.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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