[gmx-users] Problem with tpr files
jalemkul at vt.edu
Thu Jan 24 15:05:21 CET 2013
On 1/24/13 7:21 AM, James Starlight wrote:
> Dear Gromacs Users!
> In the gromacs-4.6 version I have some problems with the trp files
> obtained after reduction of atom subset via
> tpbconv -f initial.tpr -n index -o reduced.tpr
> where in index file reduced atom sub set was defined ( e.g c-alpha
> atoms from the protein only )
> then I'm using g_Covar to calculate covariance matrix from my
> trajectory also with reduced atom subset and obtain error
> g_covar -f xz.xtc -s reduced.tpr -o EDA_eigenval.xvg -v
> EDA_eigenvec.trr -av EDA_average.pdb -tu ps
> Program g_covar, VERSION 4.6
> Source code file:
> /home/own/Documents/distr/gromacs-4.6/src/gmxlib/mtop_util.c, line:
> Software inconsistency error:
> Position restraint coordinates are missing
> the same error was obtained with other commands wich also require tpr
> file as the input
> How it could be filed?
Create a .tpr file that doesn't use position restraints.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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