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