Hi George,
in case you are still looking for a solution, I could imagine that the pdb-file of a crystal structure does not exactly match the number/order of atoms in your topology file (e.g. added hydrogen atoms). I don't recall my own example exactly, but I think stripping the system until there was a 1:1 relation of reference atoms and snapshot positions before reading in the reference.pdb and issuing the rms command helped me some time ago.
Good luck
Astrid
P.S.: Did ptraj eventually give a warning/complaint concerning the reference.pdb?
----- Ursprüngliche Mail -----
Von: "George Tzotzos" <gtzotzos.me.com>
An: "AMBER Mailing List" <amber.ambermd.org>
Gesendet: Mittwoch, 4. Januar 2012 19:15:38
Betreff: [AMBER] ptaj: RMSD
Hi everybody,
I'm measuring the backbone RMSD of a 2ns equilibration trajectory against the crystal structure.
Using the VMD RMSD trajectory tool and having as reference the crystal structure I obtained the following results:
id mol avg sd min max num
0 2wc6.pdb 0.000 0.000 0.000 0.000 0
1 2wch_bal_solv.prmtop 1.222 0.084 0.987 1.481 1000
Using the following ptraj input file:
trajin equil_2ns.mdcrd.gz 1 1000 1
reference 2wc6.pdb
rms reference out equil_0-2ns.rmsd @CA,C,N
I obtain the results shown in the attached snapshot. 15+ Angstrom?
Any suggestions as to the observed discrepancy would be greatly appreciated.
Best regards
George
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 06 2012 - 06:00:09 PST
