On 3/21/13 6:30 AM, Shima Arasteh wrote:
Dears,
As I read in some other messages in mailing list, it is supposed to modify
bonds, angles and dihedrals in top file to define a peptide bond for the last
and first residues as well as other peptide bonds.
I am wondering if it is necessary to define pairs too?
If pairs are a necessary part of the force field, then yes. Look at the
formulation of peptide bonds that you have not messed with to learn what is
expected.
-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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