AMBER Archive (2008)

Subject: Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory

From: Ian (ian2craig_at_gmail.com)
Date: Wed Jun 11 2008 - 05:53:42 CDT

Thanks Vlad and David for that advice, but I've still not been able to use
ptraj to strip away atoms based on their distance from some reference atom
or residue.

To illustrate my problem, I've taken a single frame from a protein MD
simulation (using ptraj) and put it in a file called test.trj (Amber
trajectory format). I then try the following two ptraj operations:

  trajin test.trj
  strip "(:1 >@5.0)"
  trajout strip1.trj nobox

  trajin test.trj
  strip "(:1 <@5.0)"
  trajout strip2.trj nobox

Note that the first tries to strip all atoms further than 5 Angstroms from
the first residue, and the second tries to strip all atoms closer than 5
Angstroms to the first residue.

As described in the original post, the ptraj that comes with Amber9 just
freezes. The most recent ptraj (version 9.9h) executes -- but strip1.trj and
strip2.trj are identical! This is clearly not the result I expected. The
ptraj that comes with AmberTools throws a segmentation fault.

I've read the manual and tried to search the mailing list archive. I can't
figure out what I'm doing wrong here -- if you can see it, please point it
out, however obvious. I'd be very grateful. I'd also like to know if this
functionality is known to be .. not functioning.

Many thanks,

Ian.

On Fri, Jun 6, 2008 at 7:50 PM, Vlad Cojocaru <
Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:

> Sorry, of course. While writing the answer I shortly forgot about it.
> AmberTools is for free so the latest ptraj is to be found there.
>
> vlad
>
>
>
> David Case wrote:
>
> On Fri, Jun 06, 2008, Vlad Cojocaru wrote:
>
>
> I believe the ptraj from AMBER9 does not implement the new mask parser
> (I believe this type of mask is available only in the new parser). What
> I would suggest if you dont have AMBER10 is to download the stand-alone
> version of ptraj from Tom Cheatham's webpage (latest version is 9.9h I
> believe).
>
>
> Please note that ptraj is a part of the (free) AmberTools package, not
> Amber10. To get the lastest version of ptraj, you should download and install
> AmberTools from http://ambermd.org.
>
> ...dac
>
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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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