Questions about nmode Command
Hellow specialists:
I want to caculate the normal mode frequences of a protein with nmode
command.first ,I do Energy minimization in sander and got the local energy
minimum conformation Coordinate “min.rst” .then I Edit nmode script
“nmd.in”like
below:
normal mode analysis
&data
ntrun=1,
maxcyc=0,
nsave=250, nprint=250,
cut=10.0,
scnb=2.0, scee=1.2,
nvect=30, ilevel=0,
t=310.0,
and Enter the command like :
$AMBERHOME/bin/nmode -O -i nmd.in -o nmd.out -c min.rst -p Glu.prmtop -r
Glu.rst -v Glu.vecs
Then I get an error:
***************** ***************** *****************
step = 0
F = -0.526752E+02 GRDMAX = 0.525215E+01 GNORM = 0.155207E+01
E-NONB E-ELE E-HBOND E-BOND
0.11450E+02 -0.84061E+02 0.00000E+00 0.38022E+00
E-ANGLE E-DIHED E-NB14 E-EEL14
0.24024E+01 0.40266E+01 0.15051E+01 0.11621E+02
E-POL E-3BOD
0.00000E+00 0.00000E+00
Root-mean-square gradient of input coords is 1.55207279918410
This is greater than the requested maximum: 1.000000000000000E-005
Then check Each energy component of sander result and nmode result,I found
the E-EEL14 item is different, which is 38.2626 in sander. What's this
about? So this is my first queston.
Later ,I turn up the drms to 5.0 to to avoid this error,then I
got the normal
mode eigenvalues in “Glu.out”,like
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 75.455 37.957 102.989
translational 0.923 2.979 41.114
rotational 0.923 2.979 29.847
vibrational 73.608 32.000 32.027
1 -0.014
2 0.000
3 0.000
4 0.000
5 15.956
6 17.041
7 51.622 0.619 1.976 4.827
8 90.323 0.625 1.957 3.725
9 124.291 0.633 1.932 3.104
10 131.321 0.635 1.925 2.998
11 148.172 0.640 1.909 2.767
12 194.258 0.657 1.856 2.256
13 260.820 0.689 1.760 1.722
14 267.339 0.693 1.749 1.679
15 286.182 0.704 1.718 1.561
16 379.039 0.767 1.544 1.101
17 399.342 0.783 1.503 1.021
18 428.541 0.807 1.442 0.917
But I can’t get the eigenvectors in Glu.vecs, This file was empty! Where
can I got normal mode eigenvectors? So this is my second question.
thank you for your early reply!
--
---------------------------------------------------------------------
ZhangMK
+8623-63063582
Chongqing Institute of Green and Intelligent Technology of Chinese Academy
Sciences.
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Received on Sun May 04 2014 - 01:30:03 PDT
