Re: [gmx-users] Help in parametrisation

onetwo twoone21 at
Thu Jun 24 07:06:55 CEST 2010

Thanks Justin for the help,

I have Manganese in my protein with other two ligands at the active site. 
I am using GROMOS96 43a1 force field.

Mangnese may have topology similar to Magnesium 2+, What I found is that I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate the nonbond_params for ffG43a1nb.itp.

For both the other two ligands which contains phosphate and enol groups, I was able to create topology using PRODRG server.


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,
> 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

-- ========================================

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

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