Hello Ambers,
I am trying to do some binding free energy
calculations using MM_GBSA method for a DNA triplex.
For that, I have considered the duplex of the triplex
as the receptor, the third strand as ligand and the
triplex as the complex. But, the result of the mm_pbsa
show that the triplex has higher energy, which is
mainly, arises due to the electrostatic energy
(6820.2kcal/mol). The electrostatic energy of the
duplex is 1379.12 and the third strand is -263.32. For
this calculations, I have used non-bonded cut-off
distance=999. If the non-bonded cut-off distance is
set to be 9, then the electrostatic energies are
885.1, -1195.9 and -982.5 for the triplex, duplex and
third strand respectively. Because of this high
electrostatic energy, the total gas phase energy of
the triplex becomes positive. The following is the
input I have used for anal. Anybody, please tell me if
I have made any mistake.
Gas phase energy
1 0 0 0 0 1
0 0.0 0.0 0.0 0.0
1 0 2 1 25 1
999.0 2.0 1.2 1.0
0
PDB
ENERGY
GROUP
RES 1 27
END
END
STOP
In addition to this, I am getting the following error
message, while running the MM_GBSA script:
srdf: 6 singular edges
ERROR: find_SES_contact_faces: inf==0 for face 6848
sphere_mange_arete: inconcistence
ERROR: find_SES_contact_faces: inf==0 for face 7076
sphere_mange_arete: inconcistence
ERROR: find_SES_contact_faces: inf==0 for face 6737
sphere_mange_arete: inconcistence
sphere_mange_arete: inconcistence
sphere_mange_arete: inconcistence
ERROR: find_SES_contact_faces: inf==0 for face 4890
ERROR: find_SES_contact_faces: inf==0 for face 4655
ERROR: find_SES_contact_faces: inf==0 for face 2742
I will be very much thankful to you, if anybody tells
your suggestion regarding the above problems.
Thenmalar
~
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Received on Thu Mar 07 2002 - 21:13:40 PST
