[gmx-users] Dihedral copying from itp to ff

[Mark Abraham]

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.
>