Re: AMBER: file corruption with ptraj

From: Thomas E. Cheatham, III <>
Date: Mon, 18 Oct 2004 09:42:02 -0600 (Mountain Daylight Time)

> What I discovered through many attempts is that whenever I remove (strip
> water) using ptraj it corrupts the output trajectory files. For example,
> below I show the script were I removed the water trajectories:
> trajin file1.mdcrd
> trajin file2.mdcrd
> strip :WAT
> tarjout file1_2.mdcrd

If you are stripping the water, likely you want to specify the "nobox"
option to trajout to prevent writing box information. When you look at a
movie, if the first frame is good and then you see the long bonds, likely
this is due to the extra box info in the trajectory that is not in the

> box x 51.1333056 y 50.7934380 z 72.1834321
> center :1-198 origin
> image :199-398 origin center familiar

Note also that unless you are running constant volume, imaging with a set
box could be artifactual, that is unless you are trying to image to the
average box size to artificially remove box scaling fluctuation.

> box x 51.1333056 y 50.7934380 z 72.1834321

This command will effectively be ignored if the prmtop does not contain
box information

> The output file once again, gave a message saying there was a corruption
> found in the trajectory file at step #340 :

This is probably where ptraj is expecting to read in at least 6 numbers
and only finds three (the box information) where it was expected to read
atoms due to the offset problem...

Let me know if the "nobox" specification does not fix the problems.


\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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Received on Mon Oct 18 2004 - 16:53:00 PDT
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