Hi,
/I have a protein/Mg-ATP structure and I'm trying to calculate //the
binding free energy of this protein-cofactor system.
//My input is:
&general
// strip_mask=:WAT:Cl-:Cs+:IB:K+:Li+:Na+:Rb+,
startframe=1, endframe=5, interval=1,
verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
The calculation run until the end but the results are really senseless.
The .pdb files for Ligand, Rec and Complex are like this
MODEL 1
ATOM 1 HH31 ACE 1 -nan -nan -nan 0.00 0.00
ATOM 2 CH3 ACE 1 -nan -nan -nan 0.00 0.00
ATOM 3 HH32 ACE 1 -nan -nan -nan 0.00 0.00
ATOM 4 HH33 ACE 1 -nan -nan -nan 0.00 0.00
ATOM 5 C ACE 1 -nan -nan -nan 0.00 0.00
ATOM 6 O ACE 1 -nan -nan -nan 0.00 0.00
ATOM 7 N GLU 2 -nan -nan -nan 0.00 0.00
ATOM 8 H GLU 2 -nan -nan -nan 0.00 0.00
ATOM 9 CA GLU 2 -nan -nan -nan 0.00 0.00
ATOM 10 HA GLU 2 -nan -nan -nan 0.00 0.00
ATOM 11 CB GLU 2 -nan -nan -nan 0.00 0.00
ATOM 12 HB2 GLU 2 -nan -nan -nan 0.00 0.00
And in the "FINAL_RESULTS_MMPBSA.dat", I found...
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
EGB -66427.3241 0.0000 0.0000
G gas 0.0000 0.0000 0.0000
G solv -66427.3241 0.0000 0.0000
TOTAL -66427.3241 0.0000 0.0000
Receptor:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
EGB -64081.8425 0.0010 0.0004
G gas 0.0000 0.0000 0.0000
G solv -64081.8425 0.0010 0.0004
TOTAL -64081.8425 0.0010 0.0004
Ligand:
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
EGB -2345.4816 0.0000 0.0000
G gas 0.0000 0.0000 0.0000
G solv -2345.4816 0.0000 0.0000
TOTAL -2345.4816 0.0000 0.0000
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err.
of Mean
-------------------------------------------------------------------------------
VDWAALS 0.0000 0.0000 0.0000
EEL 0.0000 0.0000 0.0000
EGB 0.0000 0.0000 0.0000
ESURF 0.0000 0.0000 0.0000
DELTA G gas 0.0000 0.0000 0.0000
DELTA G solv 0.0000 0.0000 0.0000
DELTA TOTAL 0.0000 0.0000 0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
/
Can anyone tell me what i'm doing wrong? or some suggestion?
Thanks in advance,
/Chiara
/
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Received on Wed Mar 13 2013 - 11:00:03 PDT
