AMBER Archive (2002)

Subject: ptraj

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Fri Jul 26 2002 - 14:43:36 CDT

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

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