AMBER Archive (2008)

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

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Thu Nov 06 2008 - 12:31:07 CST

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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