[gmx-users] OPLS for a single zwitterionic residue
Mark.Abraham at anu.edu.au
Tue Nov 21 22:47:19 CET 2006
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!
Probably the parameterization process for OPLS/AA did not include such
an amino acid, so you will struggle to defend whatever choice you make
unless you develop the parameters yourself. Read the OPLS/AA paper and
understand the method they used. That may answer your question directly,
or give you a path to follow to develop an answer.
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