[gmx-users] Problem in PCA of protein ligand system

Wed Sep 28 07:29:37 CEST 2016

Dear Tsjerk

Thank you for the suggestion.

Best Regards
Ashutosh

On Mon, Sep 26, 2016 at 7:37 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Ashutosh,
>
> If you want to look at specific motions, like a dihedral, then just look at
> that (gmx angle).
>
> Cheers,
>
> Tsjerk
>
> On Mon, Sep 26, 2016 at 11:10 AM, ashutosh srivastava <ashu4487 at gmail.com>
> wrote:
>
> > Dear Tsjerk
> >
> > Thank you so much for the detailed explanation.
> > So is there a way to extract motions of only ligand, along a particular
> > direction (say rotation along a dihedral in ligand) from this trajectory?
> >
> > Best Regards
> > Ashutosh
> >
> > On Mon, Sep 26, 2016 at 3:52 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Ashutosh,
> > >
> > > To simplify this, let's do PCA of two balls on opposite ends of a stick
> > I'm
> > > rotating. The mean position of both ends is right at the center of
> > > rotation, and the relative positions I can describe with X and Y
> > > coordinates only. Now, the essence of PCA is the question 'which single
> > > direction can I find that explains most of the spread of my points?'.
> > Since
> > > this is pure rotation, any direction is as good as any other, so I just
> > > pick the horizontal line through the center. I then project my
> trajectory
> > > onto this axis. Surprise: I find that the principal component describes
> > > lengthening and contraction of my stick along the horizontal direction.
> > > What? Let's check the other component, orthogonal to the first. That
> too
> > > describes lengthening and contraction, but anticorrelated with the
> > > projection onto the first. The thing is, I can't ever describe a
> > > ((semi-)rigid) rotation with a single component. The projection needs
> to
> > go
> > > through the center and come out the other end, looking like a
> contraction
> > > and expansion. Likewise, the mean structure is halfway, so it's the
> most
> > > distorted configuration along the axis.
> > >
> > > I hope this clarifies your observations.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > > On Mon, Sep 26, 2016 at 4:32 AM, ashutosh srivastava <
> ashu4487 at gmail.com
> > >
> > > wrote:
> > >
> > > > Dear all
> > > >
> > > > I have performed a 200 ns simulation on a protein ligand  (MOL)
> system
> > in
> > > > gromacs 5.1.2. Is it possible to get low frequency motions of only
> the
> > > > ligand?
> > > > When I am looking at the filtered trajectory (along PC1) after
> > performing
> > > > PCA on the protein+MOL the small molecule looks distorted. There is
> an
> > > > aromatic ring in the molecule that collapses and expands during the
> > > course
> > > > of trajectory and the methyl groups are all collapsed throughout the
> > > > trajectory.
> > > > Following is the command that I am using
> > > >
> > > > covar -f "$TRAJ" -s "$TPR" -o
> > > > ck2_go289_eigval_${first_frame}_${interval}.xvg -v
> > > > ck2_go289_eigvec_${first_frame}_${interval}.trr -av
> > > > ck2_go289_eigavg_${first_frame}_${interval}.pdb -l
> > > > ck2_go289_eiglog_${first_frame}_${interval}.log -ascii
> > > > ck2_go289_eigcovar_${first_frame}_${interval}.dat -xpm
> > > > ck2_go289_eigcovar_${first_frame}_${interval}.xpm -xpma
> > > > ck2_go289_eigcovara_${first_frame}_${interval}.xpm -b $first_frame
> -e
> > > > $interval
> > > >
> > > > anaeig -v ck2_go289_eigvec_${first_frame}_${interval}.trr -f "$TRAJ"
> > -s
> > > > "$TPR" -eig ck2_go289_eigval_${first_frame}_${interval}.xvg -comp
> > > > ck2_go289_eigcomp1_${first_frame}_${interval}.xvg -rmsf
> > > > ck2_go289_eigrmsf1_${first_frame}_${interval}.xvg -proj
> > > > ck2_go289_eigproj1_${first_frame}_${interval}.xvg -filt
> > > > ck2_go289_eigfilt1_${first_frame}_${interval}.xtc -first 1 -last 1
> -b
> > > > $first_frame -e $interval
> > > >
> > > > I have also tried giving -extr option and the extracting 2000 frames
> > > along
> > > > the PC1, the molecule looks distorted even in this.
> > > >
> > > > I have tried following
> > > > 1) Fitting CA and MOL and covariance analysis on CA and MOL
> > > > 2) Fittting CA only and covariance on MOL only
> > > > 3) Fitting MOL only and covariance on MOL only
> > > > 4) Isolating the MOL trajectory separately and then performing PCA on
> > > this
> > > > trajectory.
> > > > 5) Fitting all atoms and covariance analysis on all atoms
> > (protein+MOL).
> > > >
> > > > Before all this I performed following PBC corrections on the
> > trajectory.
> > > >
> > > > trjconv -s prod_0-10.tpr -f prod_0-100.xtc -o whole_100ns.xtc -pbc
> > whole
> > > >
> > > > trjconv -s prod_0-10.tpr -f whole_100ns.xtc -o nojump_100ns.xtc -pbc
> > > nojump
> > > >
> > > > trjconv -s prod_0-10.tpr -f nojump_100ns.xtc -o
> > center_mol_ur_compact.xtc
> > > > -pbc mol -center -ur compact -n index.ndx
> > > >
> > > > trjconv -s prod_0-10.tpr -f center_mol_ur_compact.xtc -o
> > > > fit_center_mol_ur_compact.xtc -n index.ndx -fit rot+trans
> > > >
> > > > I have done mass weighted analysis and the result is the same.
> > > > In all the cases the MOL becomes distorted in the filtered
> trajectory.
> > > > In order to visualize the trajectory I am extracting the 0th frame of
> > the
> > > > trajectory (CA and MOL) from the actual trajectory and then loading
> > > > filtered trajectory on top of that.
> > > > I also tried extracting the 0th frame of filtered trajectory and then
> > > > loading the trajectory on top of that.
> > > > I have looked at the actual trajectory  and the small molecule as
> well
> > as
> > > > protein is fine in that with no weird motions.
> > > >
> > > > What am I doing wrong here?
> > > >
> > > > Kindly let me know if anymore details are required.
> > > >
> > > > Thank you
> > > >
> > > > Ashutosh.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>