Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

2011-06-16 Thread Mark Abraham
On 17/06/2011 12:33 AM, maria goranovic wrote: thought of that, but the trajectory also has HISB data .. .xtc and .trr trajectories have no atom identification. That's why lots of the tools require a .tpr or coordinate file, together with a trajectory file in order to function. Using bash, lo

Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

2011-06-16 Thread maria goranovic
thought of that, but the trajectory also has HISB data .. so I guess I will have to alter it frame by frame ? On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham wrote: > On 16/06/2011 11:01 PM, maria goranovic wrote: > >> Hi >> >> I had a simulation run with 4.0.7, using opls-aa for a protein in water

Re: [gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

2011-06-16 Thread Mark Abraham
On 16/06/2011 11:01 PM, maria goranovic wrote: Hi I had a simulation run with 4.0.7, using opls-aa for a protein in water. I now use part of the protein coordinates output from the simulation, and use pdb2gmx as: pdb2gmx -f conf.gro -ff oplsaa -ignh pdb2gmx complains that it cannot find HIS