[gmx-users] Re: Dissociation of Ligand-reg

[Justin A. Lemkul]

ITHAYARAJA wrote:
> Sir,
> 
> The simulation system consists of enzyme, two substrate and one native 
> ligand (protein, glutathione and NADPH + FAD) actually I am interested 
> in manifesting substrate (GSH of GSSG and NADP+ of NADPH) dissociation 
> from the protein after reduction reaction. I here below mentioned an 
> article reference for your notice, likewise can we do simulation work?
> 

Presumably.  Whether or not the same methods are applicable are for you to decide.

-Justin

> 
> Dong Long, Yuguang Mu, Daiwen Yang "Molecular Dynamics Simulation of 
> Ligand Dissociation
> from Liver Fatty Acid Binding Protein" Plos, 2009.
> 
> 
> 
> 
> On 13 June 2011 10:09, ITHAYARAJA <ithayaraja at gmail.com 
> <mailto:ithayaraja at gmail.com>> wrote:
> 
> 
>     Dear Sir,
> 
>     Greeting!
> 
>     I convey my thanks to your kind reply for rising whatever doubts and
>     troubles in gromacs.
> 
>     I able to do my simulation with desire ligand following your
>     instruction. Now I am interested to simulate the dissociation of
>     bound ligand particularly one molecule among three. Sir, I need your
>     help to do this dynamics study. I also went through some article
>     which refers to SMD, TMD, IMD, REMD and AFM pulling able to do the
>     job. So, Kindly instruct me which one can support gromacs for ligand
>     dissociation simulation and What are the parameter set ?
> 
>     Thanks in advance
> 
> 
>     Kind regards with,
> 
>     -- 
>     **
>     Ithayaraja M,
>     Research Scholar,
>     Department of Bionformatics,
>     Bharathiar University,
>     Coimbatore 641 046,
>     Tamil Nadu
>     India
> 
> 
> 
> 
> -- 
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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