AMBER Archive (2008)

Subject: AMBER: imaging problem

From: Marcin Krol (krol01_at_cancer.org.uk)
Date: Tue Apr 15 2008 - 06:54:30 CDT

Dear All,

I've run a 10ns MD simulation of a tetrameric protein in explicit
solvent (PBC). I used iwrap=1. Still different monomers jump away from
the others, then go back - I assume they jump to other periodic cells. I
tried to put all monomers back to the primary unit cell. I used a
modified ptraj script suggested some time ago by Prof. Cheatham (bring
first molecule to the origin, image, then center the whole solute and
image again, script given below). Since I have four monomers, I centred
and imaged each monomer separately and then the whole molecule. But it
doesn't put the monomers back to the primary cell. It shifts the whole
system (probably because of the multiple center keywords), but the
tetramer is still disrupted (3rd monomer 653-978 in another periodic
cell). I tried different commands (imgining by mask, with origin center,
without origin, etc) but never managed to get the whole tetramer back
together.
Can someone tell me what is going wrong? Any help will be great!

Many thanks
Marcin

My script is given below:

trajin N-md100.nowat.crd 1 1000 50
trajout N_md100.repacked.crd trajectory

center :1-326 mass origin
image origin center

center :327-652 mass origin
image origin center

center :653-978 mass origin
image origin center

center :979-1304 mass origin
image origin center

center :1-1304 mass origin
image origin center

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