[gmx-users] partial charge on protein

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 6 18:06:31 CEST 2009

Homa Azizian wrote:
> Hi
> there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or 
> it should better ignore this?

You should absolutely NOT ignore this problem.  You have a fractional charge of 
non-negligible magnitude.  Did you use -missing with pdb2gmx?  If so, you are 
probably not accounting for some atom that should otherwise be present.

As it stands, your system is non-realistic.


> --
> Tehran University of Medical Sciences
> www.tums.ac.ir


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


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