[AMBER] [Amber] nmode() results with imaginary frequencies

From: Guqin Shi <shi.293.osu.edu>
Date: Tue, 1 Dec 2015 18:18:17 -0500

Hi all,

I'm using nmode() to calculate entropy for protein-ligand complex. I got
results successfully but some of them has additional line seen in below:
                - Thermochemistry -

Temperature: 298.150
   Pressure: 1.000
       Mass: 11668.480
Principal moments of inertia in amu-A**2:
        809809.49 1666184.08 1773921.38
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
*found 1 imaginary frequencies*
Zero-point vibrational energy: 8667.328

             freq. E Cv S
            cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 6749.690 3252.715 3898.857
translational: 0.888 2.979 53.869
rotational: 0.888 2.979 53.610
vibrational: 9204.459 3246.757 3791.379


Is this a big problem I need to solve before I use the data? I read a
little bit it seems that it indicates the protein is in some sort of
transition state...? I used xmin() to minimize the protein to grms of
0.001. I also browsed amber mailing list and in a post from 2009, somebody
suggested that ntrun() set to 0 could solve problem. My nmode() function is
set as:
nmode(xyz,3*natm,mme2,0,0,0.0,0.0,0); where ntrun() is already set to 0.0.

Any idea or something important I missed?
Thanks a lot for your time!


Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
AMBER mailing list
Received on Tue Dec 01 2015 - 15:30:04 PST
Custom Search