Re: [gmx-users] Help in parametrisation

[onetwo]

Hello Justin,

Thanks for the reply.
Sorry to say but I chose the GROMOS force field as for that topology of the ligands could be prepared by PRODRG and I followed tutorials available for Gromacs and most of them used GROMOS forcefield and for starting, parameters used in the tutorials helped me to create .mdp file  for my problem.
I may be wrong in such choice of forefield.
I tried yesterday installing Amber utility for gromacs but when I tried  to generate topology of protein with Mangnese, It was giving same error as Mn is not present in its database as also mentioned in the following website http://ffamber.cnsm.csulb.edu/.
Any help ?
I am really thankful to you for ur time and patience.
Regards

onetwo wrote:
> 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

Assuming a transition metal "may" be similar to another species is probably a pretty poor assumption.  Prepare for lots of criticism if you proceed with that thought.

> I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I calculate the nonbond_params for ffG43a1nb.itp.
>

Refer to the other GROMOS papers for how they derive parameters for small molecules.  I've never seen a demonstration of transition metal parameterization under these force fields, though.  Perhaps you should be using an AMBER force field that contains Mn2+.  Any particular reason you think you need GROMOS?

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

Please pay careful attention to the second paragraph here:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin

>
> Regards
>
> 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.
>
> -Justin
>
>  > Thanks in advance
>  >
>  >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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