I ran into a similar problem--if I input a 20 set trajectory, it would say
"Set #21 is corrupted" and quote the last three coordinates of set 20 (which
it had successfully loaded!!). I found that this error message did not seem
to hurt the output (in my case, trajectories and average structures, not rms),
so I just started ignoring it. I'd love to know if anyone knows what this is
all about.
I found out (the hard way) that the flag "nobox" is critical for outputting
trajectories and average coordinates for non-periodic trajectories, but I
don't see that flag listed for the rms action. Did it actually generate output
for you?
Kristina
>===== Original Message From Joseph Nachman <nachman_at_hera.med.utoronto.ca>
=====
>Hello Ambers:
>
>I'm trying to use ptraj to analyze a 100 frame trajectory generated by
>Simulated Annealing in vacuo, without periodic boundary conditions, using
>sander_classic in Amber6.
>
>Here is the input:
>
>
> trajin /tmp_disk/scratch2/jnachman/yvnvqn/50/sa1_27.crd
> rms first out sa1_27.rms :105-111_at_CA
>
>
>When I run ptraj I get the following messages:
>
>Read in control variables
>Read in atom names...
>Read in charges...
>Read in masses...
>Read in IAC (atoms involved in L-J)...
>Read in NUMEX (index to excl atom list)...
>Read in NNO (index for nonbond of .type)...
>Read in residue labels...
>Read in the residue to atom pointer list...
>Read in bond parameters RK and REQ...
>Read in angle parameters TK and TEQ...
>Read in dihedral parameters PK, PN and PHASE...
>Read in SOLTY...
>Read in L-J parameters CN1 and CN2...
>Read in info for bonds w/ hydrogen...
>Read in info for bonds w/out hydrogen...
>Read in info for angles w/ hydrogen...
>Read in info for angles w/out hydrogen...
>Read in info for dihedrals w/hydrogen...
>Read in info for dihedrals w/out hydrogen...
>Read in excluded atom list...
>Read in h-bond parameters: AG, BG, and HBCUT...
>Read in atomic symbols (types)...
>Read in tree information...
>Read in the JOIN info...
>Read in the IROTAT info...
>
>ERROR in readAmberTrajectory(): Set #101 is corrupted...
>
>
>
>
>I checked the mdcrd file and it looks perfectly all right, except -
>obviously - for the fact that the box coordinates are missing (since I
>didn't use periodic boundary conditions).
>
>I wonder whether the hiccup is caused by this lack of box coordinates, and
>if so, how can I overcome this problem? I couldn't find anything in ptraj
>manual dealing with issue.
>
>Thanks in advance,
>
>Joseph
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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
>--------------------------------------------------------------------
****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu
Received on Fri Jul 26 2002 - 11:32:38 PDT
