AMBER Archive (2004)

Subject: AMBER: Imaging problem

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Jul 30 2004 - 14:05:12 CDT

Hi
I have a homodimer protein (each dimer has 99 residues), which during my
periodic box-simulations (explicit waters) separated. I then tried
Imaging using the following command:
 
trajin wt.restrt_2500

trajout wt2500imaged pdb

center :1-99 origin

image :100-198 origin center

go

 

I also tried:

trajin wt.restrt_2500

trajout wt2500imaged pdb

center :1-99

image :100-198 center

go

 

The dimers do reform, but the problem is that now there are hugh VDW
contacts between atoms. For example, I have an Oxygen from one monomer
that is 1.97A to a Nitrogen of the other monomer.

I checked the MD energy and so there is no "clashing" between the atoms
during MD. The problem only occurs when I do the "imaging".

Any help would be greatly appreciated

Cheers, Steve

 

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