Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization

From: David A Case <>
Date: Fri, 15 Aug 2014 07:17:16 -0700

On Fri, Aug 15, 2014, 张冬冬 wrote:

> Actually I'm quite sure about the underlying problem behind the results,
> which have large RMS, stars form like **** of VDW and EEL in it. I
> have checked the system structure and found that there are two atoms (
> belonging to different residues ) getting very closer (almost sitting
> on each other) and one near bond is stretched after finishing the
> minimization step two.

A wild guess: are you using SHAKE for hydrogens? You need to do this for
most Amber force fields. Beyond that, you'll have to try to figure out what
is going on with the atoms involved in the bad contact. It is possible that
you are getting a "polarization catastrophe" where two induced dipoles get too
close together. I don't have much experience with ff02 myself.


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Received on Fri Aug 15 2014 - 07:30:02 PDT
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