[gmx-users] OPLS for a single zwitterionic residue

[Ran Friedman]

Dear David,

You may want to calculate the charges using QM potential, in the same
lines as used to develop OPLS (HF 6-31G* IIRC), and then define the
residue. Given the small size of the molecule it shouldn't be to much work.

Best,
Ran.

David Nutt wrote:
> Dear all,
>
> I'm trying to simulate a zwitterionic single amino acid residue using
> the OPLS forcefield but have run into a problem with the definition of
> partial charges. Basically, the total charge of the residue following
> setup is not an integer.
>
> The problem is caused by the definition of the 'patches' for the
> standard C and N termini -- both of them modify the partial charge on
> the Calpha atom. Each patch works fine by itself (and the resulting
> total charge is an integer), but when setting up a single amino acid,
> the CA charge is changed twice and you can get two different
> (non-integer) total charges depending on whether you do the CTER or
> NTER patch first! This problem doesn't occur with the Gromos
> forcefield since the CTER patch doesn't touch the partial charge on
> the CA atom.
>
> To solve this problem, I will need to change the patch or define a new
> residue, but there are several ways in which this could be done. If
> anyone has done this before, I would be pleased to hear about how they
> did it!
>
> Thanks,
> David.
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-- 
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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