Re: [AMBER] peptide leaving box, image command not working

From: Niel Henriksen <>
Date: Tue, 15 Jun 2010 07:58:21 -0600

I believe I understand what your're describing. This has happened with some
ligand/receptor complexes I have studied. The problem was that when my receptor
got close to the box edge, the receptor got "wrapped" differently than the ligand.
This occurs since even though the receptor and ligand are in a complex, sander/pmemd
still views them to be separate entities and thus determines how to wrap them separately.

As far as I know, once you've run the simulation there is no good way to go back and
fix the problem.

My lab uses a prmtop hack to get around this problem. We change the values in
sander/pmemd into thinking that that the complex is a single molecule. This was
described in previous posts:
(I use option 1, not option 2)

I wrote a perl script to edit the prmtop automatically. Let me know if you are interested.

From: Omair A. Khan []
Sent: Monday, June 14, 2010 11:51 AM
To: AMBER Mailing List
Subject: [AMBER] peptide leaving box, image command not working

Dear All,

I'm having a very frustrating problem. I ran a 250 ns trajectory of a
protein and peptide complex with PMEMD in Amber 10. When I generated PDB
files from the restrt (saved as .xyz) files, I saw that my peptide had
drifted extremely far away in some of the structures. It's likely that it
left the primary unit cell. However, in my Sander input file, I made sure
that iwrap was set to 1. (The exact same input and production settings used
for this trajectory have worked successfully on other ones.)

Unsure as to why iwrap didn't work in the first place (it always has for my
other simulations), I tried using every possible combination of *image*, *
center*, and *rms *to correct the mdcrd output coordinate files (saved as
.crd) so that I wouldn't see these wild fluctuations. The link below
includes my topology file, one of the output crd and xyz files, and an
example ptraj script I tried using to correct the crd file. I need to
generate corrected coordinate files because they feed directly into my
scripts for further analysis.

One thing I noticed when running the ptraj script was that although most of
the coordinates in the new crd file seemed acceptable, there were a few that
had values of more than 300. It's unlikely that the peptide or the protein
has moved such a great distance in one picosecond.

The files can be downloaded here: (~200 MB)

Thanks in advance,

AMBER mailing list

AMBER mailing list
Received on Tue Jun 15 2010 - 07:00:06 PDT
Custom Search