[gmx-users] Changing Ligand coordinates to top of PDB
Justin Lemkul
jalemkul at vt.edu
Thu May 14 18:37:33 CEST 2015
On 5/14/15 1:37 AM, Raj D wrote:
> 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.
The order of the coordinate file is irrelevant with respect to the definition of
parameters in the topology.
-Justin
> 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
>>>>>>>
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>>>>>>> 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
>>>>>
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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
>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
--
==================================================
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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