Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps

From: Jianyin Shao <>
Date: Thu, 6 Nov 2008 16:48:47 -0600

Hi, Bud,

When you select atoms based on distance criteria in ptraj, you need to
provide the atom coordinates for ptraj using a "reference ref.cor" command
before other ptraj commands. Due to the reason that the ptraj determines the
atom masks at the beginning of the processing, the atom selection is not
dynamic. The rdparm cannot take "reference" as a command, so please chek
your ptraj output to make sure the atom masks are correctly selected.


Jianyin Shao

On Thu, Nov 6, 2008 at 12:31 PM, M. L. Dodson <> wrote:

> Hi folks,
> I was trying to recover a pdb of active site residues and close waters
> (using ptraj from AmberTools1.2) with the following command:
> strip "!((:1,22,144,145) | (.2478 <:4.2 & :WAT))"
> This works fine in ambmask when checked without the negating !() to
> keep the size down. I.e, ambmask should give the identify of the
> residues left after the ptraj strip command, and ambmask does identify
> the desired residues. However, ptraj drops core and gives a nonsense
> pdb file (includes a bunch of seemingly random solute and water
> atoms). Checkmask in rdparm just drops core with a segmentation fault
> after printing a whole bunch of atom strings either with or without
> the negating !().
> Is anything obviously wrong with this? Has this behavior been
> documented?
> I tried the search engine on the archive, but may have failed due to
> lack of search string foo.
> Bud Dodson
> PS,
> strip "!(:1,22,144,145)"
> works fine
> strip "!(.2478 <:4.2 & :WAT)"
> behaves the same as the whole strip mask given above.
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
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Received on Fri Dec 05 2008 - 11:08:40 PST
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