On 4/3/13 7:16 AM, Liron Cohen wrote:
After reading the manual and trying to find more information on the mailing
list. I'm still not sure about this 1-4 interactions, when I want to calculate
the energy between two groups (lets say one residue and the rest of the
protein) should I sum everything (including the 1-4 interactions) or should I
only include the SR interactions.
1-4 interactions are intramolecular and thus should not be included in
intermolecular energies. If you're using PME, decomposing the long-range
component to the electrostatics term is challenging.
-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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