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

ashutosh srivastava ashu4487 at gmail.com
Mon Sep 26 04:32:37 CEST 2016

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
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
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

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
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


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