Dear Jianyin,
Ok, the warning "empty token" comes from line 402 in mask.c and it
disappears if the mask string is ':*' instead of '*'. It seems that the
parser likes at least 4 characters in the mask string (although the
3-char string was correctly processed as well) . But (as I expected) the
warning has nothing to do with the imaging problem.
The problem also persists in the ptraj from AMBER 10.
For now, I just wanted to make this clear
vlad
Vlad Cojocaru wrote:
> 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.eml-r.villa-bosch.de
>> <mailto:Vlad.Cojocaru.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/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu <mailto:amber.scripps.edu>
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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/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
--
----------------------------------------------------------------------------
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/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------
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Received on Sun Jun 08 2008 - 06:07:35 PDT
