AMBER Archive (2008)

Subject: Re: AMBER: ptraj imaging issue

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jun 05 2008 - 03:48:43 CDT

Dear Jianyin,

Thanks for the re. Of course its not the most urgent thing and I can use
the old ptraj for imaging ... At the end its a convenience issue to not
switch between different versions for different tasks. So, I thought its
a good thing to ask about it or let people know about the problem.

The mask "*" is correctly recognized but I get this "empty token?"
warning which made me think that one of the options (either "center" or
"origin") for the image command might not be correctly applied. I would
gladly send you a copy but the trajectory is way too big (> 2GB). I
would need to make chunks first and send one small chunk for testing.
Unfortunately I dont have time now as I am preparing a talk for a
conference next week but if the problem persists and no solution is
found I can send you later on this month a traj chunk.

Cheers
vlad

Jianyin Shao wrote:
> Hi, Vlad,
>
> We changed mask parser since ptraj9.9?, maybe ptraj9.9e. There might
> be some unintended discrepancies between the two parsers. However, I
> think the new parser should be able to interpret "*" as all atoms.
> Please check the output to see if the mask actually represents any
> atoms. I am not sure why this could cause something wrong with "image"
> command as that in your case. If your files are not very big, do you
> mind sending me a copy? In the meanwhile, you can use the old ptraj if
> your main concern is to use image. Or you can replace the call of
> function processAtomMaskDetailedVH() back to processAtomMaskDetailed()
> in lines 1352 and 1359 in ptraj.c file (for ptraj9.9h, but this could
> cause problem when parsing new style masks.)
>
> Best,
>
> Jianyin
>
> On 6/4/08, *Vlad Cojocaru* <Vlad.Cojocaru_at_eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>> wrote:
>
> Dear Ambers,
>
> I have noticed a problem with the image command in ptraj9.9e and
> ptraj9.9h .
>
> When applying the script below with ptraj9.9h (the "e" subversion
> behaves the same), I got strangely looking box with one layer of
> water separated from the cubic box. Furthermore, I got an warning
> in the ptraj logfile connected to the image command ("warning:
> empty token?"). Now when I tested the same script with the ptraj
> from AMBER 9, everything worked perfectly and no warning appeared
> in the logfile (everything was absolutely identical). The trj.dcd
> is a NAMD generated trajectory with box info
>
> I couldnt test yet the ptraj from AMBER10 (or AmberTools 1.0).
>
> Is this something that has been observed by others as well ? If
> its a known problem, is it fixed in the latest released ptraj from
> AmberTools 1.0. Or maybe something has changed in the syntax of
> the image command (although the manual doesn't indicate that)?
>
> Cheers
> vlad
>
> ------------------script------------------------------------
> trajin trj.dcd
> center ":1-467" origin
> image origin center "*"
>
>
> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
> <http://eml-r.villa-bosch.de>
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++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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Amtgericht Mannheim / HRB 337446
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http://www.eml-r.org
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