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

From: David A Case <>
Date: Sat, 12 Dec 2015 22:32:03 +0100

On Tue, Dec 08, 2015, Guqin Shi wrote:
> 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...?

Make sure you set "eigp" in the nmode() call to the number of
eigenvalue/eigenvector pairs you want. Results will go to an output file
called "vecs". Look for lines with "***", to find the frequencies in cm-1.
Imaginary frequencies will be printed as negative values.

> 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!!!

We need details about how you did the minimization. Have you used the
newton() procedure from NAB.

Note that 2800 frames is likely to be way more than you need. Normal modes
are rather insensitive to the details of the geometry (assuming you are
sampling the folded region), and many fewer nmode() runs are required...try a
few and check your convergence.

...good luck...dac

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Received on Sat Dec 12 2015 - 14:00:03 PST
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