[gmx-users] g_cluster changing traj.trr file to traj.trr.tpr
etfiedler at gmail.com
Fri Jul 8 23:29:49 CEST 2011
On Jul 8, 2011, at 3:23 PM, Justin A. Lemkul wrote:
> Eric Fiedler wrote:
>> I'm running Gromacs 4.5.1. Our group uses lammps for our simulations, but I'm
>> trying to use the g_cluster tool. I used VMD to convert trajectory files to
>> .trr and .pdb format, then attempt to run g_cluster using:
>> g_cluster -f traj.pdb -s trajstart.trr -g cluster.log -cutoff 1 -fit -method
>> I get an error saying trajstart.trr.tpr does not exist, which of course it
>> doesn't. VMD can't convert to .tpr, otherwise I'd try that.
> You can't pass a trajectory file to the -s flag. The required formats are either .tpr, .pdb, or .gro. It looks like you've got your inputs (-f and -s) backwards.
>> Also, when I try to use -s trajstart.pdb for my reference frame, I get an
>> error that reads "rmsd cutoff 1 is outside range of rmsd values 1e20 to 0".
>> So I can't use the .pdb file either.
> So presumably you've passed the .pdb file to both -s and -f? That's probably the source of the problem.
>> Suggestions appreciated!
>> Eric Fiedler-- gmx-users mailing list gmx-users at 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-request at gromacs.org. Can't post? Read
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users