[gmx-users] complex topology file

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 2/10/16 10:31 PM, Sana Saeed wrote:
> My question is, even if i use Acpype , and follow the steps of making complex
> files as in tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html can
> I use these files for MD of binding free energy calculation or I have to make
> them in different way.
>

Assuming you're using the protocol using an AMBER force field instead of GROMOS, 
then probably the Acpype output is OK.  Many people use it, but I haven't so I 
can't comment on it.  But if you're going to be parametrizing new things, you 
should have a good understanding of the parent force field, what its assumptions 
and parametrization methods are, and how parameters are validated.  Then you can 
assess how good of a ligand topology you have.

-Justin

> Sana Saeed Khan,
> Teaching-Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
> On Thursday, February 11, 2016 10:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 2/10/16 8:34 PM, Sana Saeed wrote:
>  > please someone help me. i want to find out absolute binding free energy of
>  > protein ligand complex. fisrt i performed docking and selected best poses and
>  > then i made topology file of ligand with PRODRGserver. and then included itp
>  > file of ligand in Protein topology file (from pdb2gmx) , also made
>  > complex.gro as in tutorial
>  >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>  > . can i use these complex files for MD for absolute binding free energy? in
>  > some tutorials the topology file of complex is quite differently organised.
>  > please guide me, i am following decoupling and coupling steps from
>  >
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
>
>  >
>
> I already replied:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-February/103524.html
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

-- 
==================================================

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

==================================================