Dear Mustard Thanks very much for your useful notes and your reply Mohsen On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard <musta...@onid.orst.edu> wrote:
> Yeah there is so much to do. > > 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. > > > > 2. yes (you don't even need a state_B) > > > > 3. no (gromacs 4.5.x will take care of it if you setup your mdp file > correctly) > > > > 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. > > > > I know "read the manual" is the go to phrase here, but it works 95% of the > time for me. > > > > > > On December 21, 2010 at 2:08 AM mohsen ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > Dear All > > I want to calculate protein-drug binding free energy. > I read Dr.Mobley tutorial(about free energy of methan dissapearing from > water).I couldn't understand some of it's parts. > > Can I use thisr tutorial in this case(protein-drug)? > > Besides, I have a few question about that: > 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). > 2-Are these files(.top & .gro) the same for all values of lambda? > 3-Do these files(.top & .gro)change if you inversed the meaning of lambda=1 > & lambda=0? > 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? > > Please let me know the answer of my questions > Thank in advance for your reply > Sincerely yours > Mohsen > > > > TJ Mustard > Email: musta...@onid.orst.edu > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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