Dear Mustard<br>Thanks very much for your useful notes and your reply<br>Mohsen<br><br><div class="gmail_quote">On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard <span dir="ltr"><<a href="mailto:mustardt@onid.orst.edu">mustardt@onid.orst.edu</a>></span> wrote:<br>
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<p style="margin: 0px;">Yeah there is so much to do.</p>
<p style="margin: 0px;"><span>1. Build a methane in a program that allows saving of pdb. Make sure the pdb and all the atoms are correctly formated. Or find a methane pdb or gro file. I think there is one off of Dr. Mobely's website.</span></p>
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<p style="margin: 0px;"><span>2. yes (you don't even need a state_B)<br>
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<p style="margin: 0px;"><span>3. no (gromacs 4.5.x will take care of it if you setup your mdp file correctly)<br>
</span></p>
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<p style="margin: 0px;"><span>4. All you need to do is read the free energy perturbation section in the manual. You will change the settings of your mdp file (under fep) and your off. I got some rather nice values.</span></p>
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<p style="margin: 0px;">I know "read the manual" is the go to phrase here, but it works 95% of the time for me.<span> </span></p><div><div></div><div class="h5">
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On December 21, 2010 at 2:08 AM mohsen ramezanpour <<a href="mailto:ramezanpour.mohsen@gmail.com" target="_blank">ramezanpour.mohsen@gmail.com</a>> wrote:<br>
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Dear All<br>
<br>
I want to calculate protein-drug binding free energy.<br>
I read Dr.Mobley tutorial(about free energy of methan dissapearing from water).I couldn't understand some of it's parts.<br>
<br>
Can I use thisr tutorial in this case(protein-drug)?<br>
<br>
Besides, I have a few question about that:<br>
1-What do I need to use as my .top & .gro files in my commands?(with regarding my problem)docked state or separated state?for example he has used methan(separated from water).<br>
2-Are these files(.top & .gro) the same for all values of lambda?<br>
3-Do these files(.top & .gro)change if you inversed the meaning of lambda=1 & lambda=0?<br>
4-How did he define for (with which parameters) Gromacs that lambda=1 is relating to completely interacting & lambda=0 is relating to methan disappearing system?<br>
<br>
Please let me know the answer of my questions<br>
Thank in advance for your reply<br>
Sincerely yours<br>
<span style="color: rgb(136, 136, 136);">Mohsen</span>
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</div></div><font color="#888888"><p style="margin: 5px 0px; font-family: monospace; white-space: nowrap;">TJ Mustard<br>
Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a></p>
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<br>--<br>
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