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

From: M. L. Dodson <>
Date: Mon, 10 Nov 2008 12:23:17 -0600

Jianyin Shao wrote:
> PPS, thinking about this some more, your answer would seem to imply
> that the identities of the waters selected by distance would be fixed
> by the reference coordinates. That does not work very well for my
> purpose, since I wanted to see the waters come and go into and out of
> the region of the active site over the trajectory. Is this correct?
> Yes, the identities of water molecules will be fixed throughout the
> entire trajectory. With the distance criteria, the number of water
> molecules may be different for each frame. You can try the "closest"
> command in ptraj to retain a fixed number of closest water molecules.
> Jianyin

The following ptraj script gave me almost what I want, and the
difference from my ideal distance-based solution is not really very
important in the real world. (ALD is a ring-open deoxyribose residue,
and the trajectory was collected with iwrap=1)

----------------------script begin----------------------
trajin traj.gz
trajout AS_traj.pdb pdb nobox append

rms first ".CA"
closest 4 ":ALD.C1=" oxygen noimage
strip "!((:1,22,144,145) | :WAT)"

----------------------script end------------------------

Thanks again,

Bud Dodson

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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Dec 05 2008 - 14:15:05 PST
Custom Search