AMBER Archive (2009)

Subject: Re: [AMBER] rings getting planar

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Nov 26 2009 - 09:07:43 CST

On Thu, Nov 26, 2009, Jio M wrote:
>
>
>  when I relax molecule (in xleap gui interface)
> this ( ca-ca-cc-ca and cd-cc-ca-ca) force two rings to be in same
> plane {{{please correct me if I am wrong}}}. but they should not be..
> what other force field I can use for such problem..

The LEaP "relax" command uses a very simplified, hard-wired set of potential
functions. Run the minimization in sander if you want to use your custom
potential.

>
> 2) For dynamics part,, If I use the same parameters for this molecule
> and do sander minimization with restraints on solute,, output is
> normal. But when restraints are removed 1-4 EEL and EAMBER  is
> shown as stars

Stop the minimization shortly before the "stars" and examine the structure; it
looks like two atoms are almost on top of each other, and you need to figure
out which pair this is, and why.

....dac

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