[gmx-users] Energy minimization for Inositol pyrophosphate

Justin Lemkul jalemkul at vt.edu
Thu Feb 26 02:48:34 CET 2015

On 2/25/15 1:15 AM, ashish bihani wrote:
> Hello, I have understood my mistakes that I reported in previous queries of
> this string. now, I am proceeding more systematically.
> I have generated ff parameters for Inositol Pyrophosphate with the help of
> PRODRG server (as mentioned in the tutorials) as a residue and added it to

Hopefully you're not actually using raw PRODRG parameters, they're generally 
quite inadequate.

> aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals
> and impropers by imitating the format of the definitions of other residues.
> But I am not able to find a format for [ pairs ] which I believe is important
> for my experiment. Particular pairs defined in ffnonbonded.itp file of
> gromos54A7 do not have codes unlike dihedrals. If I have two columns for
> individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do
> I point the program to corresponding c6 and c12 values in ffnonbonded.itp?

The GROMOS force fields only use special pair interactions for certain 
combinations.  If you haven't parametrized these interactions, it's hard to say 
whether or not you actually need them.  Perhaps you should be looking into a 
more well established force field rather than trying to create one from scratch 
from a questionable web server.

> Secondly, the parameter file generated by PRODRG does not contain all the
> possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored
> because of some criteria or should I add them manually?

You'll have to be more specific about what's missing and why you think it should 
be there.  In general, dihedrals aren't compulsory for every possible bond, but 
the details vary from force field to force field.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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