[gmx-users] extracting from TRR

2014-09-26 Thread N. S.
Dear GMX experts, How could I extract the only state from MD-simulation .TRR (or traj.xtc) file that has the lowest RMSD from the reference protein.pdb file? Please give me a line of code in UBUNTU or the script. Thank you in advance, Happy journey through the Universe, Niyaz -- Gromacs Users

[gmx-users] apoenzyme wanted

2014-09-24 Thread N. S.
Dear Gromacs users, I study an enzyme (hydrolase), which is known to undergo some conformational changes upon substrate or inhibitor binding. Protein Data Bank at rcsb.org has only suitable entries with complex enzyme-inhibitor structures. I had got might be a stupid idea to make minimisation