Dear Justin<br>You are right,But I searched in tools and I found g_sham<br>It is very useful tool for estimating Gibbs free energy,Enthalepy ,<br>emtropy and ...<br>I think I can use from that for my calculation of binding free energy(In the other words,del G free energy of system )<br>
how do you think about g_sham?<br><br><br><br><div class="gmail_quote">On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Gromacs users<br>
<br>
I want to calculate Gibbs free energy too,but about Protein-drug binding.<br>
Please guide more clearly,what texts I need to read for learning how can I do it?<br>
</blockquote>
<br></div>
Look into the literature and nearly any of the popular simulation textbooks.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Besides,g-energy has an option for estimating free energy from trajectory file(-fee option)<br>
I thought if I had a trajectory file of binding state I could estimate binding free energy by this option.<br>
am I right?<br>
does it give me Gibbs free energy?(Is this equall to binding free energy?)<br>
</blockquote>
<br></div>
Never used this option, but from the description of the option, it calculates delta(G) relative to an ideal gas state, which sounds completely unrelated to what you want to accomplish.<br>
<br>
Besides, if g_energy could magically solve this difficult problem, no one would bother with more thorough methods, like PMF or thermodynamic integration.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
thanks in advance<br>
Mohsen<div class="im"><br>
<br>
On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
shahab shariati wrote:<br>
<br>
Hi gromacs users<br>
Can I use gromacs for obtaining Gibbs free energy of binding of<br>
protein and dna?<br>
<br>
<br>
Yes. I would suggest you read about potential of mean force<br>
calculations.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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