Re: AMBER: dynamics of isolated system

From: Dr. Yong Duan <>
Date: Tue, 29 Jul 2003 16:16:35 -0400 (EDT)

Your E(angle) is "nan" at the first step. "MM optimization"? Can you be a
bit more specific, if it is not a secret. We can not help if all we get is
vague description.
This appears to be a small molecule. You can e-mail prmtop prmcrd mdin (or
whatever the files you like) to me as attachments. I will see what I can


On Tue, 29 Jul 2003, Herbert Georg wrote:

> It's just one molecule alone. The geometry was obtained with MM
> optimization. About the VDW terms, I thought about that but, well, the
> prmtop and impcrd files were built with LEAP, and it looked ok, and if
> the molecule wasn't distorted in the process between the pdb file and
> the prmtop/impcrd files, then I don't know why this is happening.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Jul 29 2003 - 21:53:00 PDT
Custom Search