On 4/21/13 1:43 PM, Arunima Shilpi wrote:
Dear Sir
I have query as what criteria do you follow to adjust the charges of ligand
atoms in topology file (drg.itp) as you have shown in example for jz4
Assuming you are referring to my tutorial, the functional groups in the JZ4
ligand are all described within the Gromos96 parameter set used therein. The
parameterization strategy of that force field (and others) was such that once a
model compound or group has suitable parameters derived, it can be applied as a
building block for other molecules, thus the parameters are transferable between
molecules. This is not always the case for all force fields, however.
-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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