[gmx-users] Dihedral copying from itp to ff

[Raj D]

Thank you Mark, I will workout your suggestions.
Regards,
Raja
On May 12, 2015 8:50 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> I don't know if that particular functionality is supported, but if you look
> at the way the GROMOS force fields implement their parameter lookups, you
> can see that
>
> [dihedral]
> N C C O phi kphi mult
>
> just works, presumably by generating the default dihedraltype. You can only
> try
>
> [dihedral]
> N C C O type phi kphi mult
>
> or maybe
>
> N C C O type
>
> and have the parameters looked up from modified FF files. Check out manual
> 5.6.1 also.
>
> Mark
>
> On Tue, May 12, 2015 at 4:26 PM Raj D <gromacs.for.f at gmail.com> wrote:
>
> > Thanks Mark, right now I am identifying the dihedral of ligand atoms in
> top
> > file produced by pdb2gmx and replace the function type from default 9 to
> 3
> > and so the grompp process the new dihedral defined in the ffbonded.itp
> > successfully. But I would like to identify a straight solution that
> pdb2gmx
> > to identify the right function type  and do it itself in the output
> > topology file.
> > Regards,
> > Raja
> >  On May 12, 2015 7:28 PM, "Mark Abraham" <mark.j.abraham at gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > Another way to unite two .itp files is to write a script to renumber
> all
> > > the atom indices in the second molecule's .itp so that they follow on
> > from
> > > those in the first molecule. Then you can cut and paste them together.
> > >
> > > Mark
> > >
> > > On Tue, May 12, 2015 at 3:56 PM Raj D <gromacs.for.f at gmail.com> wrote:
> > >
> > > > Dear Justin,
> > > > Thanks ,I am doing it to bring the ligand and protein under one
> > molecule
> > > > type in order to apply distance restraint between atoms of ligand and
> > > amino
> > > > acids . This I am doing based on your suggestion for my earlier post
> > > >
> > > >
> > >
> >
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097280.html
> > > > .
> > > > So why always pdb2gmx write topology with proper dihedral function
> type
> > > of
> > > > 9 and how to force it to write different function type based on user
> > > entry
> > > > in ffbonded.itp file.
> > > > Regards,
> > > > Raja
> > > > On May 12, 2015 5:01 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 5/12/15 12:05 AM, Raj D wrote:
> > > > >
> > > > >> Dear User,
> > > > >> I have done MD simulation successfully with ligand.itp file
> produced
> > > by
> > > > >> Antechamber. Now I have to include the ff information of the
> ligand
> > > into
> > > > >> AMBER99SB forcefield
> > > > >> and in the process I am so for successful in creating rtp entry
> and
> > > bond
> > > > >> and angles parameter in ffbonded.itp file but I have struck in
> > copying
> > > > >> dihedral parameters data from ligand.itp to ffbonded.itp files.
> > > > >>
> > > > >
> > > > > Why is any of this necessary?  You can save yourself the hassle and
> > > just
> > > > > keep the parameters in the ligand.itp file; there's no need to copy
> > > > > anything to the parent force field.
> > > > >
> > > > > -Justin
> > > > >
> > > > >  The antechamber produced dihedral type 3 ( RB ) and the grompp
> issue
> > > the
> > > > >> ERROR like No default Proper Dih. types for all missing new
> dihedral
> > > of
> > > > >> the
> > > > >> ligands ( totally 68 errors) and if I change the function type
> from
> > 9
> > > > to 3
> > > > >> ( the default in the AMBER99SB ) the grompp sense the new
> > dihedral...
> > > > >> Please help me to get out of the issue.
> > > > >> Regards,
> > > > >> Raja
> > > > >>
> > > > >>
> > > > > --
> > > > > ==================================================
> > > > >
> > > > > 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
> > > > > http://mackerell.umaryland.edu/~jalemkul
> > > > >
> > > > > ==================================================
> > > > > --
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