[gmx-users] partial charge on protein

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 6 21:53:11 CEST 2009

Homa Azizian wrote:
> Hi 
> according to my problem about non-neglible magnitude partial charge on 
> protein, I did not use -missing option with pdb2gmx my command is:
> pdb2gmx -ignh -f .pdb -o .pdb -water spce
> what should I do to neutralize this charge?

You should probably start over and check carefully for any warnings or error 
messages.  Which force field are you using?  A charge of 0.08 sounds like a 
missing hydrogen, but that may or may not be true.


> Thank you in advance.
> --
> 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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