AMBER Archive (2001)

Subject: Re: escaping atoms....

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 09 2001 - 17:34:27 CDT

        i have just tried to do an energy minimization of a protein +
        ligand in water (in constant volume) and the minimization failed
        due to the escaping of atoms. does anyone know why this happened
        and what i could do so it doesn't happen again?
        
A simple hack that might work is to increase the size of the
box at the end of the prmtop using an editor - e.g. add 1A in
each direction.

It is necessary to know how you built the model and the
trends of the component energies for more in-depth analysis.
If there is an unreasonably stretched bond or vdw overlap,
this could generate forces that would cause minimization
problems.

Bill Ross