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, look at gmxdump -f traj.xtc 2>&1|less to learn what is there. You merely need to be confident the atom ordering hasn't changed from whatever generated the old trajectory.
so I guess I will have to alter it frame by frame ?
Even if your trajectory is some pseudo-format like .pdb or .gro, you can convert it back to one of the above easily.
Mark
On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> 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. 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 HISB. I checked that the topology files in 4.5.3 do not contain HISB, while those in 4.0.7 do. It does not suffice to create another copy of the HISE topology in the .rtp file and call it HISB, because a number of hydrogen atoms also have been renamed? What can be done? I want to use 4.5.3 because I would prefer to retain residue numbering Rename all the HISB residues in your input coordinate file to whatever OPLS/AA wants. Mark-- gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Maria G. Technical University of Denmark Copenhagen
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
