Sir,<br><br>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?<br>
<br><br>Dong Long, Yuguang Mu, Daiwen Yang "Molecular Dynamics Simulation of Ligand Dissociation<br>
from Liver Fatty Acid Binding Protein" Plos, 2009.<br><br><br><br><br><div class="gmail_quote">On 13 June 2011 10:09, ITHAYARAJA <span dir="ltr"><<a href="mailto:ithayaraja@gmail.com">ithayaraja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br clear="all">Dear Sir,<br><br>Greeting!<br><br>I convey my thanks to your kind reply for rising whatever doubts and troubles in gromacs. <br>
<br>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 ?<br>
<br>Thanks in advance<br><br><br>Kind regards with,<br><br>-- <br><font color="#888888"><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>
Tamil Nadu<br>
India<br>
</font></blockquote></div><br><br clear="all"><br>-- <br><font size="2"><b></b></font><br>Ithayaraja M,<br>Research Scholar,<br>Department of Bionformatics,<br>Bharathiar University,<br>Coimbatore 641 046,<br>Tamil Nadu<br>
India<br>