[gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much.

On Tue, Aug 1, 2017 at 7:00 AM, 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
> > >
> > > ==================================================
> > > --
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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*
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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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-- 


*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*