[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 1 16:01:56 CEST 2010

maria goranovic wrote:
> I tried pdb2gmx with an alanine pdb file, with options 5 (opls force 
> field),  0 (NH3+ n-terminus) and 0 (COO- C-terminus). When I run grompp 
> on the output from pdb2gmx, I get a total charge of -1.1. Any ideas why 
> this happens?
> The same problem is not there if one looks at a dipeptide. Why the 
> problem for a single amino acid? It looks like when pdb2gmx applies 
> patches for the N-terminus and C-terminus to the ends of a protein, it 
> changes atom types for the peptide backbone. If one uses a single amino 
> acid, the patches are applied to the same residue, and hence the odd 
> -1.1 charge? If this is so, is this not a bug?

This is not a bug.  You're choosing the wrong termini.  With OPLS, there is a 
"zwitterion" terminus option that you should be using, since a single amino acid 
with two charged termini is a zwitterion.


> Thank you for inputs,
> -maria
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen


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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