[gmx-users] OPLS for a single zwitterionic residue

Mark Abraham 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.


More information about the gromacs.org_gmx-users mailing list