[gmx-users] amide partial charges in G56A3

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 13 15:44:49 CEST 2011

> Hi there
> The amide partial charges in the share folder of gromacs G56A3ff is as 
> following
>    H                             H: +0.280  N: -0.280
>     |                              C: -0.380   O: -0.380
> C-N-C-C                      other C : 0.000
>        "
>        O
> I guess all protein people use partial charges of amide like above 
> because it is in the forcefield file? I am wondering where are those 
> numbers come from? Any reference will be great!

Anyone who uses this particular parameter set will use these partial charges, yes.


> (I know in Justin Lemkul 2010 paper he discusses about the partial 
> charges of amide. I am curious about how gromacs sign those numbers. It 
> must be good although different form gaussian calculations.)

Gromos96 parameterization uses empirical adjustment to reproduce condensed-phase 
behavior and thermodynamic properties (see paper linked above), thus most QM 
calculations will not reproduce these partial charges, as we demonstrated in 
that work.


> Thank you for your time!
> Cheers!
> Xueming


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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