AMBER Archive (2008)

Subject: Re: AMBER: ptraj imaging issue

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Jun 04 2008 - 16:25:27 CDT

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> 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://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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