Hi,
I want to get the backbone RMSD of a subset of atoms in my trajectory to
a similar subset in a different structure. These atoms are supposed to move
while some surrounding atoms stay relatively fixed.
The reference structure and my trajectory are not similar (diff. nr. of
atoms and so on and so on), but the subset is.
The way I did it so far in ptraj is the following:
""""
reference ref_structure.pdb
trajin prorun_reimaged.mdcrd
strip :WAT
strip :Na+
strip :Cl-
strip !.CA,C,O,N #### here I get rid of everything except
the backbone
RMS reference :94,146,220.CA,C,N out resultsA.list #### this step
I only use to get a fit to the fixed-atoms
RMS nofit reference :63-65.CA,C,N out resultsB.list ### here I
want to measure the actual RMSD of my moving atoms
""""
Two Problems:
1) ptraj is unhappy with the diff nr of atoms in ref and traj ... but
continues, so its ok, since its still a one-to-one match
2) the rmsd results are absolutely bogus. It looks like in the first
step where I did NOT specified "nofit" he
did no fitting or he didnt translate the frame.... I always figured
ptraj would translate the frame if no "nofit" is specified
In short: I want to first superimpose a set of relatively fixed atoms
and then measure the rmsd w/o fitting of my moving atoms.
Maybe somebody can help me out.
Thanks a lot
André
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 09 2013 - 10:30:02 PDT
