AMBER Archive (2009)

Subject: [AMBER] nab normal mode analysis has imaginary frequencies

From: Junmei Wang (
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) position-restrained GB minimization with a set of force constants: 20,
10, 5, 2, 0.0 (no restraint)
(3) two-steps nab minimization using GB to reduce the RMS-gradient to
(4) nma analysis

To solve this problem, I added one more step to do some position-restrained
GBMD (force constants are 20 and 10). But no help at all.

Any suggestion how to solve the problem?

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