Dear Amber users !
I have one more question about correct post-treatment of MD trajectory
to remove PBC artifacts using cpptraj. Here is my script :
parm protein.prmtop
trajin prod.netcdf 1 -1 1
trajout stripped_traj2.pdb
strip :WAT,Na+,Cl-
autoimage
Here are two questions :
1) How could I remove all translations/rotation of the system as the
whole in order that the protein could remain in the fixed place in the
produced multi model pbb with the aim that I could only concentrate on
its conformational motions ?
2) Would it be possible to create a new processed trajectory (in pdb)
in the reverse order compared to input netcdf file, in order that I
could see "the molecular movie" from the end to beginning ?
Many thanks in advance
Enrico
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 02 2024 - 06:00:03 PST
