AMBER Archive (2008)

Subject: Re: AMBER: Water tracking

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri May 02 2008 - 11:14:21 CDT

> I emailed yesterday about tracking a water molecule. I have created
> water trajectories using "closest" ("closest 3 :557_at_NH1 oxygen") command
> in ptraj. This seems to work fine. I get a mdcrd output of the

OK, note that the closest waters change over the course of a simulation
(i.e. the closest ones are not necessarily the same water molecule over
the course of the trajectory) so that this is different than "tracking"
a specific water model.

> trajectories. However, when I try to measure the distance between
> residue 557_at_NH1 to the first water oxygen over the trajectories I get
> this error: "./ptraj Memory fault".
>
> Trajin File.mdcrd
> Distance one time 5 :557_at_NH1 :1_at_O file.txt

Usually the waters come after the solute so I think what is causing the
core dump is that residue 1 (:1) does not have a "O" atom in it.

Note that if you simply want to track waters close to that residue, you
can use the hbond facility:

donor mask :557_at_NH1
hbond series hb out hbond_wat.out \
  solventacceptor WAT O H1 \
  solventacceptor WAT O H2 \
  time 5.0 angle 120.0 distance 3.5

[In principle you could add (before the hbond command):

acceptor WAT O H1
acceptor WAT O H2

...but this may blow memory if you have lots of water; however if it does
not, this would be a way to track "which" water molecules are interacting
when, although I do not know how useful this is...]

-- tec3

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu