Jacob Spooner wrote:
I am attempting a simulation of a drug molecule using the ffamber/gaff within
gromacs. When it comes to assigning charge groups the manual says that one
should group together nearby atoms and the groups should have a net integer
charge. Since AMBER charge parameters are obtained from QM calculations of
the specific molecule they do not form into integer charge groups like with
OPLS whose charge parameters are dictated by atom type and stay the constant
in different molecules. I was wondering if somebody who has worked with
AMBER in GROMACS could give some guidance with regards to charge group
assignment.
A quick look through some of the .rtp files from the ffamber distributions
indicates that, at least for amino acid and nucleic acid residues, each atom is
its own charge group. That probably has something to do with the underlying
theory of the force field (i.e., the derivation scheme did not use charge
groups), but you can look into the literature there to be sure.
-Justin
Thanks
Jake Spooner University of the Fraser Valley
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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