AMBER Archive (2006)

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

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jan 12 2006 - 11:25:56 CST

So it works with :462-999999: I guess 4993 was the wrong thing ...
although it is definitely the last water residue in the system ....

vlad

Thomas E. Cheatham, III wrote:

>I just got in so didn't see the e-mails until now, but...
>
>
>
>>From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
>>Reply-To: amber_at_scripps.edu
>>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:
>
>:1-461_at_C*,N*,O*,S*,P*
>
>You can check what a mask selects using "rdparm" and the checkmask
>command,
>
>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
>-/-
>/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
>\-/ BPRP295A http://www.chpc.utah.edu/~cheatham
>
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-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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