Re: [AMBER] error in nmode calculations

From: David A. Case <>
Date: Thu, 29 Mar 2012 09:09:53 -0400

On Wed, Mar 28, 2012, manikanthan bhavaraju wrote:
> The 0 frame of the complex, receptor, and ligand got converged
> properly. But for the 1st frame the complex is starting with a higher
> energy
> iter Total bad vdW elect nonpolar genBorn frms
> ff: 0 2042644456039025674220868730880.00 80645056.91

Wow, you may get a record for the highest recorded energy that is not NaN, at
10^31 kcal/mol. Everything after that as far as minimization goes will be
complete garbage.

We'd need more detailed information to help with why the coordinates are so
wrong (probably have two atoms on top of each other). Make sure that what you
are trying to do with nmode is compatible with non-nmode analysis.


AMBER mailing list
Received on Thu Mar 29 2012 - 06:30:04 PDT
Custom Search