AMBER Archive (2006)

Subject: Re: AMBER: stripping trajectories: ptraj versus Carnal

From: Thomas E. Cheatham, III (
Date: Thu Jan 12 2006 - 10:59:35 CST

I just got in so didn't see the e-mails until now, but...

> From: Vlad Cojocaru <>
> Reply-To:
> Subject: Re: AMBER: stripping trajectories: ptraj versus Carnal
> As I suspected, the problem is the sintax of the strip command: if I use
> "strip :462-4993" it doesnt work but if I use "strip :WAT" it works but
> it strips only the waters and not the ions ... It would be nice if strip
> would work with residue numbers ... maybe this qualifies as a bug report
> and it would be considered for next release of ptraj ...

strip :462-999999 should work just fine; I use this all the time. Note
that ptraj outputs information on what it thinks it selected for each
command. What did the output state? If you want more voluminous
information, turn up the prnlev, i.e.

prnlev 6

in the ptraj script. Regarding selecting NOT hydrogens, I admit that this
is tricky with the current parser. The next release has a new parser
(from Victor Hornak at Stony Brook) that overcomes these deficiencies.
What I would try is to select all atoms begining with C, N, O, S or P:


You can check what a mask selects using "rdparm" and the checkmask

checkmask :1-461_at_C*,N*,O*,S*,P*

Good luck.

\-/ 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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