AMBER Archive (2008)

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

From: M. L. Dodson (
Date: Fri Nov 07 2008 - 17:15:06 CST

On Fri, Nov 07, 2008 at 10:24:03AM -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

I'll have to experiment to see if I can do a strip and closest in the
same script. I won't have a prmtop file (or be able to easily
generate one) if I do the strip first, then have to do another run to
get the waters, although I should be able to do the closest in a first
run, then (after generating a prmtop file with the correct number of
waters) do the strip in a second run. Best to try to do them both at
the same time, though. In a worst case scenario, I figured out how to
do it with a ptraj run to get the solute residues followed by invoking
a pdbcat input pipe in a perl script on the resulting multimodel pdb
(generated by resp) to strip the waters.


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
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