Re: [gmx-users] free energy of methan disappearing:tutorial

Dear Mustard Thanks very much for your useful notes and your reply Mohsen On Tue, Dec 28, 2010 at 7:48 PM, TJ Mustard 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 meth

Re: [gmx-users] free energy of methan disappearing:tutorial

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

[gmx-users] free energy of methan disappearing:tutorial

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 nee