[gmx-users] ligand topology

Wed Aug 2 00:12:55 CEST 2017

I have found

However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs
nothing
at all but *[http://www.python.org Python]*.

At the moment, *acpype* is only available for download via *svn*:

  * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype`

Yet, if some reason you cannot use *svn*, one still can get *acpype* with:

  * `wget http://acpype.googlecode.com/svn/trunk/acpype.py`

But be aware that one may run in extra troubles and I am not willing to
support
this way.

== To Test ==

At folder *acpype/test*, type:

  * `../acpype.py -i FFF.pdb`

It'll create a folder called *FFF.acpype*, and inside it one may find
topology
files for GROMACS and CNS/XPLOR.

On Tue, Aug 1, 2017 at 3:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Have you read the acpype documentation before trying to use it?
>
> Mark
>
> On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan <
> za.parash at gmail.com>
> wrote:
>
> > Dear Sir
> >
> > I have just use acpype.py -i OAI.pdb
> > I am getting the error:
> > ERROR: no 'antechamber' executable!
> > ERROR: no 'antechamber' executable... aborting !
> > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> > ==> HINT2: is 'antechamber' in your $PATH?
> >     What 'which antechamber' in your terminal says?
> >     'alias' doesn't work for ACPYPE.
> > ACPYPE FAILED: 1
> > Total time of execution: less than a second
> >
> > I am thinking that I have to install amber. But I dont want to do that.
> Is
> > there any way that I can create ligand topology for gaff.
> >
> >
> >
> > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> > >
> > >> Ok, you should not mix and match forcefields, ¿but in the case of
> > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> > >>
> > >
> > > GAFF is compatible with AMBER (by design).  My comments were warning
> that
> > > one should not use AMBER for a protein in concert with GROMOS for a
> > ligand.
> > >
> > > -Justin
> > >
> > > Best regards.
> > >> Lucio Montero.
> > >>
> > >> Enviado desde Correo para Windows 10
> > >>
> > >> De: Alan
> > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> > >> Para: Gromacs
> > >> Asunto: Re: [gmx-users] ligand topology
> > >>
> > >> Please this GitHub link is totally outdated and not linked in any
> sense
> > to
> > >> the original authors.
> > >>
> > >> Get the correct ACPYPE here:
> > >>
> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> > >> stable/ccpn/python/acpype acpype
> > >>
> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shekfeh at gmail.com>
> wrote:
> > >>
> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff
> is
> > >>> simply amber ff for small molecules.
> > >>> You have to get first amber tools. The last release is amber tools 16
> > >>> Get the source code from here :
> > >>> http://ambermd.org/AmberTools16-get.html
> > >>>
> > >>> after installation you can use antechamber for creating the
> > >>> small-molecule
> > >>> parameters
> > >>>
> > >>> later, you can use a nice free program called ACEPYP, made to convert
> > >>> amber
> > >>> parameters to gromacs toplogyget the code from here:
> > >>>
> > >>> https://github.com/t-/acpype
> > >>>
> > >>> Regards
> > >>>
> > >>>
> > >>>
> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> > >>> za.parash at gmail.com> wrote:
> > >>>
> > >>> Dear Sir
> > >>>>
> > >>>> Thank you very much for your reply. Can you give me any link or
> > >>>>
> > >>> suggestion
> > >>>
> > >>>> that i can learn for amber force field for protein and ligand.
> > >>>>
> > >>>> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalemkul at vt.edu>
> > wrote:
> > >>>>
> > >>>>
> > >>>>>
> > >>>>> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >>>>>
> > >>>>> Dear Sir
> > >>>>>>
> > >>>>>> I am new for protein-ligand complex. I want amber force field
> (ff03)
> > >>>>>>
> > >>>>> for
> > >>>
> > >>>> my
> > >>>>>> protein, tip3p for water model and gaff (General Amber force
> field)
> > >>>>>>
> > >>>>> for
> > >>>
> > >>>> ligand. I do not know how to produce gaff force field from pdb and
> > >>>>>>
> > >>>>> then
> > >>>
> > >>>> convert for gromacs topology.
> > >>>>>>
> > >>>>>> I have tried ff03 with gromos ligand topology and tip3p water
> model
> > >>>>>>
> > >>>>>> it gives me the error:
> > >>>>>> atomtype OM not found
> > >>>>>>
> > >>>>>> and when I have tried ff03 with gromos topology and spc water
> model
> > it
> > >>>>>> gives me the error like:
> > >>>>>> atomtype HW not found.
> > >>>>>>
> > >>>>>> Can anyone help me about it?
> > >>>>>>
> > >>>>>>
> > >>>>>> You can't mix and match force fields; it's fundamentally wrong.
> You
> > >>>>>
> > >>>> need
> > >>>
> > >>>> to develop ligand parameters that are consistent with the parent
> > >>>>>
> > >>>> protein
> > >>>
> > >>>> force field.  Various tools exist for different force fields, with
> > >>>>>
> > >>>> varying
> > >>>>
> > >>>>> degrees of reliability.
> > >>>>>
> > >>>>> -Justin
> > >>>>>
> > >>>>> --
> > >>>>> ==================================================
> > >>>>>
> > >>>>> 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.
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>> --
> > >>>>
> > >>>>
> > >>>> *Mohammad Zahidul Hossain Khan Graduate student**Department of
> > Physics*
> > >>>> *Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
> > >>>> * Skype: parash.khan2*
> > >>>> *Cell: +12085967165*
> > >>>> --
> > >>>> 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.
> > >>>>
> > >>>>
> > >>>
> > >>>
> > >>> --
> > >>> Dr. rer. nat. Suhaib Shekfeh
> > >>> PhD in Computational Drug Design and Medicinal Chemistry
> > >>> Oleariusstr. 11, Halle (Saale), Germany
> > >>> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> > >>> --
> > >>> 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.
> > >>>
> > >>>
> > >>
> > >>
> > >>
> > > --
> > > ==================================================
> > >
> > > 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.
> >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > 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.
> --
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>
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-- 

*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*