[gmx-users] Dihedral copying from itp to ff

[Raj D]

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
> > >
> > > ==================================================
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>