AMBER Archive (2006)

Subject: Re: AMBER: acidifying a water box

From: Eric Shamay (
Date: Fri Sep 15 2006 - 03:49:15 CDT

The problem turned out to be trivial, as pointed out in a reply to my
original post. Two molecules were overlapped and kept the system from
continuing. Thank you all for spotting the problem!


> > 2) A script then handles population of the (26 angstrom cubic) system
> > (attached - out1.pdb)
> Of key concern is step (2) above. How is this generated and where are the
> ions placed? From the minimization output, initially you have extremely
> high VDW (which implies overlap) which then relaxes to overly stretch
> bonds and likely has overlapping atoms (oxygens) which lack vdw radii so
> you get a charge/polarization catastrophe.

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