AMBER Archive (2006)

Subject: Re: AMBER: Interbox interactions

From: Thomas Cheatham (
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

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


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to