[gmx-users] for a single amino acid with NH3+ and COO- terminii, pdb2gmx gives a total charge of -1.1 in OPLSAA ?
mariagoranovic at gmail.com
Tue Jun 1 16:56:56 CEST 2010
that makes sense, thank you Justin
On Tue, Jun 1, 2010 at 4:01 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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 G.
>> Technical University of Denmark
> 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
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Technical University of Denmark
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