AMBER Archive (2009)Subject: [AMBER] nab normal mode analysis has imaginary frequencies
From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Oct 14 2009  11:05:06 CDT
Hi, Everyone,
When I ran normal mode analysis using nab for a set of ~100 residues protein
structures, I found many of them have imaginary frequencies. Here is my
calculation protocol:
(1) remove waters, ions, and generate topologies
(2) positionrestrained GB minimization with a set of force constants: 20,
10, 5, 2, 0.0 (no restraint)
(3) twosteps nab minimization using GB to reduce the RMSgradient to
~1.0e13
(4) nma analysis
To solve this problem, I added one more step to do some positionrestrained
GBMD (force constants are 20 and 10). But no help at all.
Any suggestion how to solve the problem?
Junmei
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