Hi Jason,
thanks for the response. This question might be silly but... where can I
check the actual printed frequencies...? I only have one output file from
nmode(). BTW, I used nab to calculate nmode(). I attached the output here.
Is the frequency in it? Or I need to look for it some where else.
Thanks!
Guqin
2015-12-01 22:05 GMT-05:00 Jason Swails <jason.swails.gmail.com>:
> On Tue, Dec 1, 2015 at 6:18 PM, Guqin Shi <shi.293.osu.edu> wrote:
>
> > 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!
> >
>
> Check the actual printed frequencies. Remember that 6 frequencies
> *should* be zero -- corresponding to the 3 translational and 3 rotational
> degrees of freedom. If these eigenvalues are negative (i.e., an imaginary
> frequency), rather than 0, this doesn't really matter too much since those
> modes are omitted anyway. However, if the 7th mode is imaginary, you
> probably need a stricter minimization tolerance.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Wed Dec 02 2015 - 06:30:06 PST
