[AMBER] Query regarding Ligand Binding Metalloprotein with MCPB.py

From: Abhilash J <md.scfbio.gmail.com>
Date: Thu, 8 Dec 2016 11:04:21 +0530

Hi everyone!

   I am having an issue with parameter generation of metal ion containing
   I am working with Magnesium ion. Using MCPB.py i got force constant as
negative and the distance between the atoms has increased from 2.0 to 3.7
   The bond in this case is an water oxygen and Magnesium ion.
   Is this acceptable. If not what corrections are required.

For bondtype: M1-Y5. There are 1 bond(s) in this type:
  The bond length(s) is(are): [3.7528]
  The average bond length is: 3.7528 Angstrom.
  The force constant(s) is(are): [-3.8]
  The average force constant is: -3.8 Kcal*mol^-1*A^-2.
  *The average force constant is negative, treat is as 0.0.


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Received on Wed Dec 07 2016 - 22:00:03 PST
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