Re: [gmx-users] drug-enzyme simulation.

Hi Neha, I guess you're referring to John Kerrigans tutorial, but it would usually help if you specified the one you're using. I think the tutorial should have a sentence stating that the ligand mayb be seen away from the protein during the simulations, but that that is due to the periodic boundar

Re: [gmx-users] drug-enzyme simulation.

Many thanks Justin, It worked! 2009/3/29 Justin A. Lemkul : > > > Neha Gandhi wrote: >> >> Hi List, >> >> 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated >> annealing followed by  production runs of 5ns usng NPT and PBC and >> PME.. After 5ns, the protein moves far away from th

Re: [gmx-users] drug-enzyme simulation.

Neha Gandhi wrote: Hi List, 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated annealing followed by production runs of 5ns usng NPT and PBC and PME.. After 5ns, the protein moves far away from the ligand. I checked the 4ns gro files, the ligand and protein are bound together

[gmx-users] drug-enzyme simulation.

Hi List, 1) I m running a drug -enzyme simulation. I ran 62 ps of simulated annealing followed by production runs of 5ns usng NPT and PBC and PME.. After 5ns, the protein moves far away from the ligand. I checked the 4ns gro files, the ligand and protein are bound together, but its only that 5ns

[gmx-users] Drug-Enzyme simulation

Dear GMXION, I already posted problem regarding drug-enzyme simulation using OPLSA ff for a drug whose topolgy computed from PRGDRG server. But no solution yet to me. I absolutly followed each steps of drug-enzyme simulation tutorial of GMX, in addition I also played

Re: [gmx-users] Drug-Enzyme simulation

Have included gromos forcefield (depends which one you used in prgdrg) header file (.h) in front of your topology and make the topology complete with reference to chapter 5 in manual. Yang Ye raja wrote: Dear GMXION, I already posted problem regarding drug-enzyme simulation using