[gmx-users] Help in parametrisation

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 23 17:42:05 CEST 2010

onetwo wrote:
> Hello All,
> I am new in this field, and I want to do simulation study on one of the 
> protein conatining a metal ion and study its ability to form 
> co-oridnation bond with other ligand, which is not defined in GROMOS 
> force field which I have tried. If this choice of force field is correct 
> for such type of study ?
> I have read Gromacs Manual Chapter 5, also I am following this gromacs 
> mailing list for quite some time to get a help on how to include a new 
> metal ion or a new ligand in their simulation and they have been refered 
> to refer to the 
> http://www.gromacs.org/Documentation/How-tos/Parameterization,
> but in this its not mentioned that how to actually do parameterization
> neither in manual it has been told on how to generate it ( due 
> apologies,,I know, I may be wrong )

The manual will not cover every possible topic.  Parameterization is described 
in the primary literature for the force field you wish you use.  "GROMOS" is not 
very specific - there are numerous parameter sets within this class of force field.

> and it is more difficult for a person like me who doesnt have much 
> knowledge in this field, so if someone can please help me guiding how to 
> do parameterisation, I know this is not a trivial task, but still help 
> in this regard may help many other fellow users besides me.

Aside from telling you to read all the literature you can, there's not much more 
help anyone can do to help you.  You haven't described very well what your 
system is.  What kind of functional groups are in your ligand?  If the 
functional groups are shared with existing parameters, then you'll have a rather 
easy time constructing a topology.  What type of metal ion is it?  If you're 
dealing with a transition metal, using a standard MM force field may not work 
very well.  Note the "Exotic Species" heading on the page you quoted above.


> Thanks in advance
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>


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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