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 - 11:13:58 CST

Hi Thomas,

 Thanks for the reply ... I didn't try with :462-999999 but I tried many
times with :462-4993 and the output was never right ... I checked the
ptraj output as well and it always looked as if the output is not
restricted to the first 461 residues (both for atomic fluctuations and
for the mdcrd file).... I also noticed that the output trajectory had
much more frames than the initial one.... I got rid of all the problems
by masking :WAT,Na+ (to get rid of waters and ions) and it works fine
now ....

 Of course it is possible that I've done something wrong ... maybe the
4993 was not right ..I don't know but if you say that it works for you
all the time, probably I overlooked something ...
 I will try with :462-999999 and I'll let you know if it works ...

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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