Re: [AMBER] MD simulation of protein with Calcium ion

From: Catein Catherine <>
Date: Mon, 21 Feb 2011 18:36:14 +0800

Dear Sir/Madam,
I have done a caloritm measurement on a binding between two proteins, and a protein with DNA.
Experimentally, they are in the found to be -10 and -16 kcal/mol, respectively.
I also do the MM-GBSA binding energies for the pairs of data, however, they were found to be -61 and -120 kcal/mol.
Is it well know that MM-GBSA tends to overestimate the binding energies? Can I rationizal the enhanced binding energies or give reasons why they are different so large?
I thought it could be due to salt was added in the experiment, ~ 0.2M NaCl. So, I add salt concentrate to ~ 0.2M. However, the theoretically energy only down to -50 and -100 kcal/mol, still far away from the experimental results. Any suggestions on the source of error?
Best regards,
AMBER mailing list
Received on Mon Feb 21 2011 - 03:00:03 PST
Custom Search