On 12/4/13 9:06 AM, panzu wrote:
so How do I convert from .pdb to .gro the ?
You don't technically need one:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File
If you prefer to use .gro format, just convert with editconf. The job of
pdb2gmx is to produce a topology; the output of a force field-compliant
structure is a side effect. You already have a matching structure and a
topology, so there's no need to run pdb2gmx.
-Justin
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
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