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><font color="#888888">Mohsen</font>