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 <ithayar...@gmail.com
<mailto:ithayar...@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
--
========================================
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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