[gmx-users] Problem with tpr files

[Justin Lemkul]

On 1/24/13 9:44 AM, James Starlight wrote:
> Justin,
>
> thanks. I've not known that posres were defined in the tpr file as well.
>

Sure, how else would mdrun know what to do? :)

> 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).
>

If I had any insight into that issue, I would have posted before.  Let's not 
pollute threads with unrelated stuff, but it doesn't sound like a bug to me at 
all; average structures need not have any physical significance.

-Justin

> 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
>>
>> ========================================
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-- 
========================================

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

========================================