[gmx-users] Problem with tpr files

[James Starlight]

Justin,

the problem is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtained dynamics picture of my protein with
broken geometry (its look loke my protein was shrunken). But when I
compared eigenvectors ( produced by g__covar) with the the results of
the same cov.analysis where there were no such problems in filter.xtc
I obtained full coverage in the same modes ( so g_covar in both cases
produce apropriate cov.matrix and the problem only in g_anaeig .


James


2013/1/24 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> ========================================
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