AMBER Archive (2005)

Subject: Re: AMBER: minimization.out

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 09 2005 - 13:53:41 CST

On Wed, Feb 09, 2005, Gustavo Pierdominici Sottile wrote:

> Hi, I wrote because I have a problem with the energy plot because it goes
> up.

You definitely should use a larger cutoff: try 15 Ang. or so.

You system appears to be trapped in a very bad configuration, that it cannot
get out of. Look at what is going on the vicinity of atom 2210 (SG), which
always has a very big local force. The electrostatic energy is very large
and negative, which looks to me like a warning signal. Use LEaP or ptraj to
look for bad contacts in your structure (or do this visually).

...dac

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