AMBER Archive (2006)

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

From: Chng Choon-Peng (
Date: Thu Mar 02 2006 - 18:27:15 CST

Dear Prof Cheatham,

     Thank you very much for your prompt reply and clarification.
I've searched the archives but found no posting on this matter.
So, I can continue to use the standalone version but switch to the
AMBER distribution for missing features, w/o worrying about differences
in results.
I hope this posting is also useful to all other users of PTRAJ, which
I must admit is a great tool!

  Also, I hope to clarify to all that I did not re-post my query,
resulting in the duplicated email.
Probably something wrong with my department's mail server
or a problem with Apple Mail (which I hope not!).
I seek your understanding.

with thanks,

On 2006/03/03, at 8:47, Thomas Cheatham wrote:

>> 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!!!
> --tom
> \-/ 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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Choon-Peng CHNG
Doctoral Student (Yr 1)
Dept of Computational Biology, Grad Sch of Frontier Science
The University of Tokyo
Affiliated with
Lab. of Molecular Design (Prof KITAO Akio)
Room 107, Institute of Molecular and Cellular Biosciences
1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
Tel: +81 03-5841-1472

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