[gmx-users] Dihedral copying from itp to ff

tarak karmakar tarak20489 at gmail.com
Sat Jul 11 06:20:30 CEST 2015 

Dear Justin and Mark,

I also need to impose a distance restraints between COM of protein active
site residues and COM of a ligand. But the problem is I am using an .itp
file generated from acpype. While I use it externally I can not impose the
distance restraints between the protein and the ligand. Then, I tried to
include the parameters of the ligand to specific files present in the
amber99sb-ildn directory.

I tried the following,
atomtypes.atp => atomtypes (gaff) of the ligand molecule are appended.
aminoacids.rtp => generated a new .rtp entry for the ligand molecule,
ffnonbonded.itp => non-bonded parameters are appended
ffbonded.itp     => copied and pasted the bond, angle parameters

Now, the problem I am facing with the dihedral, the implementations of RB
type (type 3) and proper dihedral type 9.
It seems pdb2gmx does not read the dihedrals specified in the ffbonded.itp
for the ligand molecule.

Would you like to suggest me something related to this?

@ Raja
Could you able to merge the force-field parameter files?

Thanks,
Tarak



On Wed, May 13, 2015 at 12:31 PM, Raj D <gromacs.for.f at gmail.com> wrote:

> Dear Mark,
> I also identified that there is no improper dihedral terms produced for the
> ligand by pdb2gmx ....I checked top file , it has all proper dihedral terms
> defined but only thing is that manual intervention to change the function
> type from 9 to 3 but I have defined all improper in ffbonded.itp for
> ligands atom types which is not written in the top file...
> Regards,
> Raja
> On May 12, 2015 9:07 PM, "Raj D" <gromacs.for.f at gmail.com> wrote:
>
> > 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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