On 6/13/12 8:20 AM, delara aghaie wrote:
Dear Justin
If we do not get error when using command pdb2gmx, and so having the .top and
.gro files, Can we make sure that every thing is ok with our pdb file or maybe
there exists some other checks to be done on pdb?
If pdb2gmx produces no error, then the contents of the initial coordinate file
matched the expectations of the force field and thus the topology and resulting
structure are fine.
-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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