[gmx-users] ligand topology

Wed Aug 2 00:00:58 CEST 2017

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 Please this GitHub link is totally outdated and not linked in any sense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
> >>>>>
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> >>>>> /Mailing_Lists/GMX-Users_List before posting!
> >>>>>
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> >>>>>
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> 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
> >>>>
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> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> 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
> >>> --
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> >>>
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> >>>
> >>>
> >>
> >>
> >>
> > --
> > ==================================================
> >
> > 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
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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*
> --
> Gromacs Users mailing list
>
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