[gmx-users] Changing Ligand coordinates to top of PDB

Thu May 14 07:37:18 CEST 2015

Dear user ,
I am going to have coordinates of non standard residues like ligand and
iron at top of the pdb file before protein coordinates since pdb2gmx unable
to process user defined bonded terms in the ffbonded.itp file. This way I
could insert a fixed set of new bonded terms for the new ligand  into the
topol.top file as produced by pdb2gmx for all simulations ( various mutants
of the same protein) without altering the atom numbers for each simulation.
I would like to have experts opinion is it a legitimate way of doing things
in gromacs  ? I afraid will it cause any unseen issue in the gromacs study
later.
Regards,
Raja
On May 13, 2015 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
>>> > > > >
>>> > > > > ==================================================
>>> > > > > --
>>> > > > > 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
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>>> > 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
>>>
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send a mail to gmx-users-request at gromacs.org.
 On May 13, 2015 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
>>> > > > >
>>> > > > > ==================================================
>>> > > > > --
>>> > > > > 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.
>>>
>>