[gmx-users] Problem with tpr files

James Starlight jmsstarlight at gmail.com
Thu Jan 24 13:21:03 CET 2013

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?


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