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?
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 15 2015 - 05:00:02 PDT
