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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>
<p style="margin: 0px;"><span> </span></p>
<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 />
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<p style="margin: 0px;"><span> </span></p>
<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>
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<p style="margin: 0px;"><span><br />
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<br />
On December 21, 2010 at 2:08 AM mohsen ramezanpour <ramezanpour.mohsen@gmail.com> wrote:<br />
<br />
<blockquote type="cite" style="margin-left: 0px; padding-left: 10px; border-left: solid 1px blue;">
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: #888888;">Mohsen</span>
</blockquote>
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<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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