[gmx-users] g_cluster changing traj.trr file to traj.trr.tpr

[Eric Fiedler]

Fixed!

Thank you!

On Jul 8, 2011, at 3:23 PM, Justin A. Lemkul wrote:

> 
> 
> Eric Fiedler wrote:
>> Hi,
>> 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
>> linkage
>> 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.
> 
> -Justin
> 
>> 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
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> 
> -- 
> ========================================
> 
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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