Re: [AMBER] strange output from vacuum minimization

From: David A Case <>
Date: Wed, 15 Jul 2015 07:42:07 -0400

On Wed, Jul 15, 2015, Albert wrote:
> When I import the structure into VMD, I noticed that it looks very
> strange: there are many atom clashes.... Here I've attached a screenshot
> for it. The initial structure is a crystal structure and it was prepare
> well before I set up the system.

It is hard to see much from the image you attached. There is one very
long bond (at the lower left): as a start, figure out which atoms are
involved, and see if that helps you to debug the problem. You should also
give details about how you imported the structure into VMD: did you create
a pdb-format file, or use the parm and restart files?


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Received on Wed Jul 15 2015 - 05:00:02 PDT
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