[gmx-users] charge group assignment with AMBER parameters

Jacob Spooner Jacob.Spooner at ufv.ca
Fri Mar 19 23:30:21 CET 2010

>>> "Justin A. Lemkul" <jalemkul at vt.edu> 3/18/2010 9:35 AM >>>

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.


Thank you for your response.  I had also noticed that each atom is its won residue in the ffamber .rtp file.
  I was under the impression that it was incorrect to have each atom as its own charge group as it 
would give strange effects due to the cutoff.  I am not so clear on my understanding of charge groups
but if I were using PME electrostatics would I obviously produce questionable results by having each atom
as its own charge group?  Your comments are greatly appreciated


> Thanks
> Jake Spooner University of the Fraser Valley


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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