[AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues

From: Yew Mun Yip <yipy0005.gmail.com>
Date: Tue, 19 Mar 2013 11:54:52 +0800

Hi, I was conducting alanine scanning on a peptide with 26 residues with
MMPBSA.py. The energy values obtained for the middle 24 residues were find,
but when I mutated the terminal residues to alanine and conduct alanine
scanning, the values were way too huge and the usual error message was
observed:

WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS. CHECK YOUR
INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE (check
differences)!

Therefore, I wish to ask if there is a way to overcome this problem or
terminal residues just can't be done with MMPBSA alanine scanning.

Thanks. 

-- 
Regards
Yip Yew Mun
Graduate, Masters
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Mon Mar 18 2013 - 21:00:03 PDT
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