AMBER Archive (2006)

Subject: Re: AMBER: Interbox interactions

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Oct 17 2006 - 10:34:50 CDT

> Does anyone know of a script/programme that can be used to perform
> interbox contact analyses from an MD trajectory? I would like to find out
> whether my solute (dodecasaccharide) is making contacts with its images.

There are a couple of ways to do this.

(1) Use the "distance" command in ptraj(); this implicitly images (unless
disabled) and will give insight into the shortest distance measured. So,
if you look at the end-to-end distance of your sugar, assuming it is not
folded, you could see short distances to the periodic images.

distance e1 :1 :10 out end-to-end.dat

(2) Build a series of PDB files with shifted images... [See the archives
for a script to do this, but basically...]

  ptraj prmtop << EOF
  trajin restrt.1
  trajout restrt_111.pdb pdb
  image origin xoffset 1 yoffset 1 zoffset 1
  EOF

...will build a PDB file imaged and shifted by one unit cell in each
direction... Then you can manually look at the interactions.

--tom

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