[AMBER] [Amber] Imaginary Frequencies from nmode()

From: Guqin Shi <shi.293.osu.edu>
Date: Tue, 8 Dec 2015 16:19:53 -0500

Hi all,

I've posted before because of imaginary frequencies seen in nmode() output
when i was doing normal mode analysis. I was suggested to check the "actual
printed frequencies" to find out which frequency is "imaginary". But I
didn't find a way to check the actual frequencies.. at least not in nmode()
output...? Any tips on where I should look for? Or maybe re-run the nmode()
and add some options?

Another problem came out after I carefully checked my results. I used
xmin() in nab to minimize protein-ligand complex. I set grms to 0.001. Out
of 2800+ frames, around 50 cannot be minimized to 0.001. I had to elevated
grms to 0.01 and that worked out for these 50 frames. Problem is, there's
intersection of these 50 frames and frames with more than 2 imaginary
frequencies from nmode()... Previously I was suggested that I might need a
stricter grms but apparently it wouldn't work out... My case is a 100
residue protein, majority is beta-sheet but with quite a few loops. Anybody
had met similar problem before...? Any tips or suggestion..? Thanks a lot!!!


Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
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Received on Tue Dec 08 2015 - 13:30:05 PST
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