AMBER Archive (2008)

Subject: Re: AMBER: Problem running implicit minimization

From: Thomas Cheatham (
Date: Tue Mar 04 2008 - 17:47:50 CST

> I'm concerned about the steric clashes throwing the energetics of my system
> off-course. What if I try to minimize my system in vacuum beforehand?

Of course, you can try this... Also, sometimes if atoms are overlapped
(within their vdw sphere) and of opposite charge, you can cause molecular
mechanics nuclear fusion. Use ptraj and the checkoverlap command:

  ptraj prmtop << EOF

If you see lot's of close contacts, what I have done in the past is to
minimize first with electrostatics turned off...

   imin=1, maxcyc = 500, ncyc = 500,
  type='ELEC', value1 = 0.0,
 &rst iat = 0, &end

Note that the electrostatics will not be exactly zero, but this will
remove overlaps often sufficiently for continuing (however overlaps could
be symptoms of a deeper problem in the setup of the initial coordinates).

-- tec3
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to