[gmx-users] Dihedral copying from itp to ff

[Raj D]

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
>> > > > >
>> > > > > ==================================================
>> > > > > --
>> > > > > 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.
>> > >
>> > --
>> > 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.
>>
>