On 1/30/13 3:27 PM, az kalsom wrote:
hi,
i wanted to know, what s simple way to correct the topology generated by
PROGRG server
i have read the paper mentioned in tutorial , but still i am nt able to
correct the file
please help me, should all CH3 CH2 charge ne made zero ?
Not necessarily. Deriving parameters for the Gromos96 force fields is a
somewhat ill-defined process, as iterative empirical refinements are often used.
Building blocks of common functional groups are generally transferable between
molecules, and recent papers have suggested parameters for many non-protein
groups. There are probably a dozen or so papers that I would consider necessary
reading before you should attempt to parameterize any molecule under Gromos96.
-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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