AMBER Archive (2004)

Subject: Re: AMBER: RMSD calculations in ptraj and Carnal

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Mon Jun 21 2004 - 10:07:57 CDT

I tried mass-weighting, and rhe results were identical to those woithout
mass weighting, which is as expected, since I'm calculating RMSDs only for
CAs.

What puzzles me is that the is that the RMSDs calculated by ptraj seem to
have no relation whatsoever to those calculated by hand (and thesame holds
true for Carnal):

RMSD(manual):

    1 2.05
    2 3.20
    3 3.63
    4 5.22
    5 4.04

RMSD(ptraj):

    1.00 2.04581
    2.00 2.15204
    3.00 2.50675
    4.00 3.22698
    5.00 0.81087

RMSD(carnal)

L0 8.693087e-03
L0 3.986790e-03
L0 2.426629e-03
L0 1.264287e-02
L0 1.153996e-02

The inputs I used are:

ptraj:

trajin 1.xyz
trajin 2.xyz
trajin 3.xyz
trajin 4.xyz
trajin 5.xyz
reference minhm.xyz
rms reference out test.rms :106-110_at_CA

Carnal:

FILES_IN
  PARM p1 1spshm.top;
  STREAM s1 1.xyz 2.xyz 3.xyz 4.xyz 5.xyz;
  STATIC ref_set minhm.xyz;
FILES_OUT
  TABLE t1 table.rms;
DECLARE
  GROUP grpid ((ATOM TYPE CA) & (RES 106-110));
  RMS fit1 grpid s1 ref_set;
OUTPUT
  TABLE t1 fit1;
END

All the structures are already fitted, since most of the structure was
kept fixed (ibelly option in sander-classic, Amber6), and only a few
residues allowed to move.

Any help and ideas welcome!

Thanks in advance,

Joseph

 On Tue, 15 Jun 2004, Thomas E. Cheatham, III wrote:

>
> By default, ptraj RMS fits *without* mass weighting. To do mass
> weighting, simply add the "mass" keyword. Back a long time ago when testing, carnal
> and ptraj give equivalent RMSd results (~1995) and the routines have not
> changed significantly since then.
>
> rms first mass out rms.dat @CA
>
>
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Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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