AMBER Archive (2006)

Subject: Re: AMBER: question about building molecules

From: David A. Case (
Date: Sun Oct 08 2006 - 11:31:27 CDT

On Sun, Oct 08, 2006, Rita Cassia wrote:
> I had taken a look with VMD how those structures look like and I had seen
> that 2 Pheophorbides were crossing each other.
> Unfortunately, when I used NAMD to start my simulation with 0 K, NAMD
> stopped the simulation, saying that a certain atom was moving too fast and
> as consequence other atoms too...

You could try a minimization first, rather than MD. That might help fix up
a bad initial structure. However, if the "crossing" is quite bad, this might
not help either.

....good luck...dac

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