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 <jalem...@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 <jalem...@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@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-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ======================================== > > 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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
