[gmx-users] OPLS for a single zwitterionic residue

David Nutt David.Nutt at iwr.uni-heidelberg.de
Tue Nov 21 14:40:33 CET 2006

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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