[gmx-users] Re: OPLS for a single zwitterionic residue

David Nutt David.Nutt at iwr.uni-heidelberg.de
Wed Nov 22 07:52:38 CET 2006

Dear all,

Thanks for the suggestions. I actually solved the problem myself, so 
here's the solution:

OPLS has other N and C terminal patches, including 'ZWITTERION_NH3+' and 
'ZWITTERION_COO-'. These are designed for exactly my situation and both 
set the CA charge to the same value. In the case of proline and 
glycine, there are even amino-acid-specific zwitterionic patches (see 
ffoplsaa-n.tdb and ffoplsaa-c.tdb).


From: David Nutt <David.Nutt at iwr.uni-heidelberg.de>
Subject: [gmx-users] OPLS for a single zwitterionic residue

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!


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