[gmx-users] Strange total charge for a single ASP system in OPLS

Farid Sa'adedin fsaadedi at staffmail.ed.ac.uk
Tue Dec 13 15:51:05 CET 2005

Check your pdb carefully there is a probably missing residue(s) causing 
this odd charge.


Quoting eladp at hplus.tau.ac.il:

> Hello all,
> I want to perform a simulation of just ASP in opls.
> after "pdb2gmx" I get a charge of -1.11
> I think the problem is in the charge of CA which is 0.04 while in a 
> protein it
> is 0.14
> When I do "pdb2gmx -ter" and select ZWITTERION NH3+ and COO- then the charges
> seem to be ok (0.15 this time) with a total charge of -1, which is good.
> Is it a bug?
> What is the difference between the regular NH3+ and the ZWITTERION_NH3+ ?
> Thanks to anyone who responds.
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Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Edinburgh EH9 1QH

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