AMBER Archive (2008)

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

From: Vlad Cojocaru (
Date: Fri Jun 06 2008 - 04:59:54 CDT

Dear Ian,

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

Compile it (its easy) and use it instead of the ptraj from AMBER9.


Ian wrote:
> Hello All,
> I am having difficulties using ptraj (v9.0) to strip a trajectory so
> that the only atoms remaining are those within a given distance of a
> particular residue. According to the ambmask section of the AMBER 9
> manual, this should be possible using something like:
> strip [:45 <@5.0]
> However, ptraj just seems to freeze when executing this command, both
> for a large protein trajectory and a completely unrelated trajectory
> of a small (8 residue) peptide. By "freeze", I mean there is no
> activity (output/messages) for at least 10 minutes. Without
> parentheses [], the above example just strips out the atoms of residue
> 45. Likewise if I replace the parentheses with double quotes (this
> should apparently force the use of a newer parser).
> I have used the "checkmask" command in rdparm as a second check on all
> this, and get the same behavior.
> Is it possible to perform this kind of operation with ptraj? If so,
> what I am doing wrong here?
> Any help would be greatly appreciated,
> Ian.

Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


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