AMBER Archive (2006)

Subject: Re: AMBER: Which PTRAJ distribution to use?

From: Thomas Cheatham (
Date: Thu Mar 02 2006 - 17:47:51 CST

> I have downloaded PTRAJ v6.5 from Prof Cheatham's website:
> and installed it but I'm also aware that AMBER8 ships with PTRAJ
> included.
> Though the standalone version seems to be newer (2003),
> there are new programs added into the suite inside the AMBER
> distribution.
> So, I'm confused over which is the better distribution to use?
> It seems that AMBER developers added new functionality that
> is absent from the standalone version.
> Also, are bug fixes applied concurrently to both distributions?

I am completely responsible for the confusion here. To answer your
question, it depends on what you want to do. AMBER8 added the very nice
matrix facility of Holger Gohlke; this directly links a number of Fortran
routines from AMBER. Although in principle (ignoring copyright issues for
the moment) I could have copied these and put them into the stand-alone
ptraj version. I did not do this.

For the routines available in each version, the results should be
equivalent EXCEPT for the "nofit" option of ptraj in v6.5 (standalone).

Very soon (we hope) there will be an updated version (with AMBER 9.0) that
brings the two versions closer to compatibility. I'll try to update the
stand-alone version soon as well.

I hope this helps and if you have specific questions about what may and
may not work as hoped in ptraj, feel free to e-mail me or the list.

Sorry for the confusion!!!


\-/ 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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