Dear gmx-users, I am trying to extract the ED of a trajectory of protein-DNA complex. I have done the simulation in AMBER and renamed the trajectory to .g87 format. i extracted out a PDB from first frame of the trajectory and use this as toplogy file.
Diagonalising the eigen vector: g_covar -f nowat.g87 -s evxone.pdb -fit -v eigen -o eigenval I selected the gromos g87 format with box info. least square fit i done with protein and diagonalised with C-alpha atoms alone. Projection: g_anaeig -v eigen.trr -s evxone.pdb -f nowat.g87 -proj proj.xvg -comp comp.xvg -last 10 The output i get is huge value against each of eigen vector. I viewed this projection in IED, it shows movement of the whole molecule along one plane in both negative and positive axis, in which the topology file (PDB) is at centre and the trajectory on eigen vector move away from it. But if i take a sample output from website (IED itself), it shows motion in a restricted manner(only the backbone is moving and not the positional displacement of whole molecule ). why it is so?. i thought my molecule is moving inside the box while simulation, hence i fit all the trajectory frames to the initial frame, but the same trend is seen. my projection values were: 0.0000 -15.78773 10.0000 -24.27282 20.0000 -27.06960 30.0000 -26.87637 40.0000 -25.94341 50.0000 -20.00264 60.0000 -18.31344 70.0000 -9.77106 80.0000 -7.00634 90.0000 -3.74432 100.0000 -6.99674 110.0000 -4.79401 120.0000 -12.33676 130.0000 -5.88940 140.0000 -8.95927 150.0000 -14.07851 .............. ............. and so on. What can be the mistake in the projection. I am seeing projection values which were low for most simulation. Regards
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
