AMBER Archive (2002)

Subject: RE: ptraj

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Fri Jul 26 2002 - 15:14:53 CDT

Yes, it did generate output and at first glance it looks reasonable, so I
suppose one just has to ignore this message.

Thanks,

Joseph

On Fri, 26 Jul 2002, Kristina Furse wrote:

> 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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> >
> >
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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
> 

-- 
--------------------------------------------------------------------
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
--------------------------------------------------------------------