AMBER Archive (2008)

Subject: RE: AMBER: MM-PBSA and delphi

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Jun 09 2008 - 14:58:28 CDT


Hi,all:

I got eigen_covar.dat by *.in file as below

rms first @CA
matrix covar name cvmat @CA out cvmat.dat
analyze matrix cvmat out eigen_covar.dat vecs 2

And the result looks like:

Eigenvector file: COVAR
 1623 1623
 38.97089 75.42463 66.16009 40.27604 73.00539 65.09814
40.47714
 70.43796 67.23996 43.39385 68.11298 67.93465 42.27330
64.68720
 ... ...
****
 1 6682.90154
 0.02344 -0.00701 -0.00270 0.00799 -0.00716 -0.00631
-0.00676
-0.01184 -0.01257 -0.00844 -0.01400 -0.01116 -0.00726
-0.01468
 ... ...
****
 2 1594.29113
-0.01981 0.00691 -0.01829 0.00485 0.00860 -0.00840
0.02343
 0.01712 0.00291 0.02034 0.01255 0.00100 0.01601
0.01468
 ... ...

The second and third parts seem to describe the first and second
eigenvector, but I'm not sure the mean of the first part? Could anybody
point me out?

Thanks in advance,

Qi

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