XUEMING TANG wrote:
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.
http://dx.doi.org/10.1002/jcc.20090
(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.
-Justin
Thank you for your time!
Cheers!
Xueming
--
========================================
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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