Dear all,
When I calculate the binding energy for protein-ligand complex using
mmpbsa, I feel confused. The following is my questions:
1. Before running nmode_prefix.in, sanmin_prefix.in will be run firstly.
When drms is 0.001, there is the negative energy to the endpoint in
sanmin_prefix.out, this energy seems right. But continue running
nmode_prefix.in, there is something wrong. Two outfile results are
-----------------------------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
16100 -2.1171E+01 1.5806E-03 8.6477E-02 C16 7243
BOND = 160.8856 ANGLE = 858.6115 DIHED =
3406.0208
VDWAALS = -4677.6959 EEL = -3015.1629 HBOND =
0.0000
1-4 VDW = 1656.3245 1-4 EEL = 1589.8453 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
16150 -2.1172E+01 1.4602E-03 4.2277E-02 C16 7243
BOND = 160.8854 ANGLE = 858.6097 DIHED =
3406.0211
VDWAALS = -4677.6800 EEL = -3015.1732 HBOND =
0.0000
1-4 VDW = 1656.3200 1-4 EEL = 1589.8453 RESTRAINT =
0.0000
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
16165 -2.1172E+01 9.1959E-04 1.3384E-02 CD 6614
BOND = 160.8850 ANGLE = 858.6083 DIHED =
3406.0219
VDWAALS = -4677.6759 EEL = -3015.1748 HBOND =
0.0000
1-4 VDW = 1656.3175 1-4 EEL = 1589.8461 RESTRAINT =
0.0000
----------------------------------------------------------------------------
***************** ***************** *****************
step = 0
F = -0.212511E+02 GRDMAX = 0.302408E+01 GNORM = 0.290194E-01
E-NONB E-ELE E-HBOND E-BOND
-0.46777E+04 -0.30152E+04 0.00000E+00
0.16088E+03
E-ANGLE E-DIHED E-NB14 E-EEL14
0.85853E+03 0.34060E+04 0.16563E+04
0.15898E+04
E-POL E-3BOD
0.00000E+00 0.00000E+00
Root-mean-square gradient of input coords is 2.901944456148840E-002
This is greater than the requested maximum: 1.000000000000000E-002
----------------------------------------------------------------------------
==============================================
The first question: why nmode cann't work well?
==============================================
However, when drms is 0.0001, there is the positive energy to the endpoint
in sanmin_prefix.out.
And David in the my previous email pointed out "Be sure to check that the
first six
modes are close to zero (say less than 1 cm**-1 or so), since you will be
at what is only an approximate minimum." I don't understand its meaning.
Can someone explain this to me?
===============================================
The second question: how to choose the right value of drms?
===============================================
2. I use sander to minimize this point. From the first step, ENERGY is
negative. The minimization works well and the result is ok.
While I use mmpbsa to minimize this point. From the firt step, ENERGY
is positive. I don't know how large difference between sander and mmpbsa.
How to explain this?
Please give me some suggestions.
Thank you in advance.
zhangli
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Received on Wed Dec 21 2005 - 02:53:00 PST
