[gmx-users] no non bonded parameters from PRODRG

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 30 19:16:12 CEST 2010

Jennifer Williams wrote:
> Hi,
> I am trying to create .top files for some complex organic molecules 
> using the PRODRG server and the gromos 96 forcefield. PRODRG gives me 
> bonded parameters (stretching, angle bending, torsions) etc but no 
> lennard jones parameters (sigma, epsilon) or charges.

I don't know how this is possible.  Atom types imply LJ parameters, and the 
charges should be written to the [atoms] directive.  If they're not, then it 
sounds like PRODRG failed.  Do you have any unsupported atom types?  Also be 
wary of the charges and charge groups PRODRG produces, the results are often 

> Where can I get the non bonded terms from? Does it make sense to extract 
> these values from the OPLS forcefield or elsewhere when I am using 
> gromas 96 forcefield to get the bonded parameters. I am wary of 
> cobbelling forcefield parameters together from different sources,

Don't bother looking at OPLS for anything if you're trying to use Gromos96. 
Look for relevant atom types in the Gromos96 parameter sets.  If they're not 
there, you should be looking for a different force field, or be prepared to 
spend a significant amount of time in parameterization.


> Thanks


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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