Re: [AMBER] Amber 11 Installment problem

From: Jian Yin <janeyin600.gmail.com>
Date: Thu, 21 Feb 2013 17:44:34 -0800

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 21 2013 - 18:00:02 PST
Custom Search