[gmx-users] Help in parametrisation

[Justin A. Lemkul]

onetwo wrote:
> 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.

There's a lesson to be learned here.  There is no substitute for doing your 
homework - reading about all the force fields, their underlying theory and 
assumptions, and work that demonstrates their advantages and limitations.  You 
must always defend your choices to a critical audience (i.e., reviewers) and "I 
saw it in a tutorial" is never going to be good enough :)

> 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/.

A tip: when posting error messages, quote the command you are using and the 
actual error message you receive.  I have no idea what you're talking about 
here.  True, manganese is not included in the ffamber ports, that much is 
already stated.  What you should try at this point is a simple web search. 
Google is your friend.  The first search result for "amber manganese" (without 
the quotes) is probably useful...

-Justin

> 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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-- 
========================================

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

========================================