[gmx-users] ligand topology

[Suhaib Shekfeh]

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