[gmx-users] Replacing the PRODRG charges

Marc F. Lensink lensink at bigre.ulb.ac.be
Thu Jun 4 22:28:43 CEST 2009

On Thu, Jun 04, 2009 at 03:46:59PM -0400, Justin A. Lemkul wrote:
> Lucio Ricardo Montero Valenzuela wrote:
>> The target forcefield will be G43a1. But I would move to more recent
>> versions of GROMOS 53a5 or 53a6.
> A more empirical charge assignment is often a reasonable starting point for 
> assigning GROMOS charges.  As I understand it, quantum calculations were 
> only done to get electron densities around each atom in various functional 
> groups; the subsequent parameterization was done empirically.  You must 
> then verify that the parameters match some condensed-phase criteria (the 
> force field references will tell you what types).
> I have gotten reasonable results based on assigning charges from comparable 
> functional groups within the building blocks in, i.e. ffG53a6.rtp.

I can second that.  charge transfer from comparable functional works
adequately for the gromos force field.  for opls/aa I've achieved
satisfactory results with resp charges.  I expect those will work well
for amber too.  compatibility between resp charges and the gromos
force field is not straightforward.

in any case, _any_ (new) parameterization needs to be verified and


Marc F. Lensink (Ph.D.)
Structure and Function of Biological Membranes            SFMB
Centre for Structural Biology and Bioinformatics          CSBB
Université Libre de Bruxelles (ULB)     marc.lensink at ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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