AMBER Archive (2006)

Subject: Re: AMBER: Trimming ptraj output

From: Thomas E. Cheatham, III (
Date: Fri Jan 13 2006 - 11:37:45 CST

> I'm switching over to use ptraj from carnal. Carnal has an option in the
> FILES_OUT section allowing the user to only output every n snapshots:
> e.g.
> COORD crd ./nowat.crd CRD MOD n;
> Is there a way to do this with ptraj, other than by altering the trajin
> lines? I don't want to do this as this will affect the analysis of rmsd
> etc.

At present, no, but this is a good idea; I've often had the problem of
wanting every 10th frame, yet my trajin coordinates are not necessarily
divisible by 10 so it is a nightmare to set up the trajin. The easy
alternative is simply to allow specification of this on the trajout. I
should have thought of that :-)

It would also be nice to have multiple trajout commands (this will be
ready soon).

> Also, a question to the author. Is it possible to stop ptraj checking
> all the input files at the beginning of the run. My trajin files are

I agree that the checking is tedious and I have a version in the works
that avoids this. The new AMBER release will also support a NetCDF binary
file that will also alleviate some of these issues (with size, accuracy
and speed of processing).

> Maybe just a simple check that the file exists would be possible rather

The reason I check at present is to figure out how many frames are present
so I can allocate memory; the new way is to allocate memory in blocks
(say 1000 frames) and if you blow memory, expand it (realloc).

> than a complete run though as this didn't catch my mistake with
> mismatched parameter and trajectory files!!

To avoid this, I usually do a simple run with one trajin line with 1 2 1
appended (i.e. only do 2 frames). Not perfect, but it works. The new
version will be available with the release of AMBER 9.0 slated for March


\-/ 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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