[gmx-users] Problem with tpr files

[James Starlight]

Justin,

thanks. I've not known that posres were defined in the tpr file as well.

By the way could you make your suggestion in my another topic which
I've posted some days ago about problem with the g_anaeig  ( below I
coppy that issue).

There is some bug  with g_anaeig the souce of which I could not fully
understand.   I have problems when I perform PCA of X-ray data set.
Below you can my workflow.


g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last 8
g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
eigrmsfPCA.xvg -filt


here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
structures of my protein (only main chain atoms are included)
ref_pdb is the first frame of that trajectory


As the result I've obtained reasonable eigenvalues and aigenvectors
from g_covar BUT when I check filter trajectory ( produced by
g_anaeig) fitted it to the ref.pdb or to the averaged structure in
both cases I've obtained very distorted geometry of the  protein in
thefiltered trajectory. I have no such problems in case of PCA of MD
trajectory ( when  -f trajectory.trr is from the md snapshots not from
x-ray structures)


How it could be fixed ?

2013/1/24 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> ========================================
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists