AMBER Archive (2008)

Subject: Re: AMBER: ptraj: new mask parser

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Jan 24 2008 - 12:19:25 CST

Hi Jianyin,

Thanks ....Yes ... for sure ... There are ways to get the heavy atoms
using the old parser, either as you said or ":467-999999@~H*". I was
just trying to find out why the new parser is not properly working in
the ptraj version from AMBER9 (although the manual says it should work)
... In fact, I was trying to teach a student and for not confusing him I
was trying to use the new parser (as described in ambmask). That's how I
realized it doesnt work and the student was even more confused as I
needed to go back to the old parser ... .... That's why I asked actually ...

I thought this bug might have been fixed in the meantime but it seems
that it wasnt ..

Thanks anyhow

Best
vlad

Jianyin Shao wrote:

> There might be bugs in ptraj, especially in the mask parser. :P
> But using the following command should get the heavy atoms you want:
>
> ":1-466_at_C*,N*,O*,P*"
>
> Hope that helps.
>
> Jianyin
>
> On 1/23/08, *Vlad Cojocaru* <Vlad.Cojocaru_at_eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>> wrote:
>
> Dear amber users,
>
> I was trying tu use the following mask string in ptraj (the version
> distributed with AMBER 9)
>
> ":1-466 & !@H="
>
> to select the heavy atoms of a protein. According to the AMBER 9
> manual
> this should work if enclosed in double quotes (which I did). However I
> always get an error saying "the = symbol wasnt recognized"
>
> The "=" symbol is described in the manual as an accepted mask
> wildcard
> in the new mask parser.
>
> Could somebody tell me why is this happening? Is there a bug that I am
> not aware of ?
>
> Thanks
>
> vlad
>
> --
> ----------------------------------------------------------------------------
>
> 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://r.villa-bosch.de>
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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>
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> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
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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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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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