[gmx-users] Cgenff generated force field problem

[Prabir Khatua]

Thanks Justin for the reply.

On Sat, Jun 15, 2019 at 6:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/13/19 8:02 PM, Prabir Khatua wrote:
> > Hi Gromacs Users,
> >
> > I am trying to do a protein-ligand simulation where the force field of
> the
> > ligand has been generated by cgenff. I have manually edited the protein
> > .top file, which has been generated  by pdb2gmx, by adding the lines
> > #include .prm and #include .itp at appropriate positions. However, I am
> > getting a list of warning while I am trying to prepare .tpr file like
> >
> > WARNING 10 [file lau.prm, line 43]:
> >    Overriding Proper Dih. parameters.
> >    Use dihedraltype 9 to allow several multiplicity terms. Only
> consecutive
> >    lines are combined. Non-consective lines overwrite each other.
> >
> >    old:                                          0 0.452709 4 0 0.452709
> 4
> >    new: CG321    CG321    CG321    CG331     9     0.000000     0.853118
> > 5
> >
> > After careful examination, I have come to know that this is happening due
> > to the fact that these are already there in the parent force field file.
> > However, I have some dihedral angle force field parameters for the ligand
> > with same atom type, multiplicty as that of the protein but a slight
> > variation in the value of kphi. Therefore, I think I probably have to
> > delete the lines that are exactly matching with that of parent protein
> > force field from the ligand prm file and to keep the lines those are not
> > matching. I am wondering whether doing this will solve my problem and
> will
> > not have any impact on the results. Please suggest me whether I am going
> to
> > do the right thing or I should do something else. Any help would be
> > appreciated.
>
> The parameter from the parent force field should be used, but be careful
> because apparently your topology does not make use of the same CGenFF
> version as the C36 port. The online server tends to be somewhat outdated
> relative to what we can provide via our force field port. Thus, some
> parameters may have changed between versions.
>
> -Justin
>
> > Thanks in advance,
> >
> > Prabir
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*