AMBER Archive (2009)

Subject: Re: [AMBER] ptraj problem

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Apr 03 2009 - 15:23:21 CDT

> I am trying to use ptraj to determine the distance as a function of time
> from a water hydrogen to a serine hydroxyl in a pmemd simulation. The box
> of waters contains more than 9999 WATs. The water I am interested in is
> listed as B 533 in the ptraj output for the pdb file. My ptraj
> input file to determine the distance as a function of time follows:
>
> ptraj atpts_nowat_c0.5_init.top << eof
> ? trajin atpts_nowat_c0.5_md_500ps.crd 1 500 1
> ? distance file3 :231_at_OG :B533_at_H1 out og_h1.dat
> ? eof

The residues numbering/chain ID's are not retained by LEaP or sleap so
ptraj have no idea which water is :B533. (Note that following Chimera
syntax we would refer to it as :555.B).

The waters are numbered sequentially after the final residues of solute;
you will have to figure out which water refers to the one in question.

The next question is why would you want this distance as likely the waters
exchange and then the water will randomly move throughout the box. If you
want to see hydration at OG (or determine whether the water moves away),
I would use the hbond analysis (and/or grid for visualization).

  donor :231_at_OG
  hbond series hbond out hbond_wat.out \
    solventacceptor WAT O H1 \
    solventacceptor WAT O H2 \
    time 1.0 angle -1.0 distance 3.5

This will show how long (and how many) waters were around the site of
interest.

--tec3

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber