Hi Astrid,
Many thanks for the clue. I guessed that it was a problem of "matching of numer/order of atoms" although I don't know the nature of the mismatch. I used tleap to generate a new reference pdb from the reference topology file. Using this new reference pdb returns results as expected (see snapshot).
Once again many thanks for the useful suggestion
Best regards
George
On Jan 6, 2012, at 2:49 PM, Astrid Maaß wrote:
> 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
>
>
>
>
>
>
>
>
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Received on Fri Jan 06 2012 - 10:30:02 PST
