[gmx-users] Problem with tpr files

Justin Lemkul 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:
> 932
>
> 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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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