AMBER Archive (2006)

Subject: Re: AMBER: problems with ptraj

From: Thomas Cheatham (
Date: Thu Aug 10 2006 - 14:25:18 CDT

> trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
> trajout ./sh3_cryst_long_1_1000.mdcrd
> go
> The output was the following:
> [...]
> Successfully completed readParm.
> PTRAJ: Processing input file...
> Input is from file sh3_cryst_long_cut.ptraj
> PTRAJ: trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd
> Checking coordinates: ./sh3_cryst_NTV_100200ps_orest.mdcrd
> Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd) with mode (r)
> WARNING in checkCoordinates(): Could not open file (./sh3_cryst_NTV_100200ps_orest.mdcrd)
> WARNING in ptrajSetupIO(): trajin ./sh3_cryst_NTV_100200ps_orest.mdcrd, cannot open file...

The file opening routines are rather generic and use a wrapped version
of the fopen() command to open the file name associated with the string.
If a .Z or .gz or .bz2 extension on the filename is present, the file is
decompressed as appropriate.

It will fail if you do not have read access to the file or the string does
not point to the correct path to the file. Assuming you could look at the
file (as pointed out by Professor Case), are you running ptraj while in
the same directory as the file? Was the ptraj input script built on
windows (such that the filename may have spurious line terminators???).
If the ptraj input script was built under windows/dos, you can see the
funny line terminators (in UNIX land) with the "od -c" command,

od -c sh3_cryst_long_cut.ptraj

if you see \r\n at the end of each line, this may be confusing ptraj.

Otherwise, I do not have a clue.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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