Subject: normal modes problem/CHARMM

From: Anil Korkut <ak2048/at/columbia.edu>
Date: Mon, 12 Jul 2004 13:21:09 -0400 (EDT)

I am doing an NMA calculation for a protein with 3000 atoms using charmm
simulation package.

I minimized my structure to a gradient of 1e-6 with 2000 steps of sttepest
descent followed by about 8000 steps of ABNR.

I know that the first six normal modes should have zero frequency.

However, I got no frequency values for the first two normal modes!!!!

The translational and rotational modes start at mode 3 and the vibrational
modes start at mode 9 instead of 7.

The frequency values are
VIBRAN> PRINT NORM MODE 1 THRU 16 DIPO

NORMAL MODES

1********** 2********** 3 -0.01 4 -0.01 5 0.00
6 0.00 7 0.00 8 0.01 9 1.51 10 1.76
11 2.40 12 3.03 13 3.40 14 3.76 15 4.05
16 4.29

I have done the same calculation with a different force field (opls-ua)
using TINKER and results were as expected (i.e. no blank modes, no 
negative
eigenvalues)

The nomal mode 7 from tinker has very similar freq. value to normal mode 9
> from charmm.

I also used BPTI as a sample protein and the same problem exists.

Does anyone have any idea what is going wrong here?

I can post my script, if anyone is interested.

Thanks

______________________________________________________________
Anil Korkut
Dept of Biochemistry and Mol. Biophysics
Columbia University,
630 West 168th St, BB204
New York, NY 10032
office ph (212) 305 1846
______________________________________________________________