Hello Changqing,
I just checked the structures you sent me. To me they are exactly the same
since the value of RMSD is 0 and I assume that you were not sending the
same picture with different names. I agree with Bill that you might have
format problems or simply some incorrect settings in
your visualization software.
Good luck~
Jane
On Wed, Feb 20, 2013 at 7:14 PM, Changqing Yan <ycqchemical.gmail.com>wrote:
> Hi everyone,
>
> I have completed installment of Amber 11. However, when I run a
> minimization of a protein, the pdb structure from the last trajectory of
> minimization seems creepy. Some atoms in the structure are very close to
> each other. So when you look at it, it seems there are many small clusters
> in one protein structure. Does anyone else encounter this problem? What is
> the problem and how to fix that? Thx.
>
> Rgds,
> C.Q.yAN
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Received on Thu Feb 21 2013 - 18:00:02 PST
