[gmx-users] Thr -> Met in TI calculation

Dear GMX users, I want to calculate the relative binding free energy between a small molecule binding to a protein of Wild Type and Thr -> Met using TI, so how should I prepare the topology files of the protein using for TI calculation? Any suggestions will be highly appreciated? All the be

[gmx-users] FES and FE molecule topology

Hello All, Could some one please help me in introducing Fe2+ and FES molecule in protein for simulation studies. But before starting it, I am not able to generate topology file for the same. I have tried to use HICUP database and used CNS topology file. but it is still not working. Please help Th

Re: [gmx-users] Helix Tilt Calculation

Thanks a lot XAvier! On Sat, Jun 5, 2010 at 2:10 PM, XAvier Periole wrote: > > Yes, > or inverse your sections from the index! > > On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote: > > Thanks XAvier and George for the reply. Yes the N and C terminus are on > the opposite sides of the bilayer

Re: [gmx-users] Helix Tilt Calculation

Yes, or inverse your sections from the index! On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote: Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct? Regards

Re: [gmx-users] Helix Tilt Calculation

Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct? Regards, Anirban On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili wrote: > Hi, > > Your 150 degree angle is