Dear all,
In our system, the Magnesium ions are included, so I try to use QM/MM-GBSA method to obtain much more accurate result. The receptor is included one Magnesium ion and protein, and the ligand is ATP with another Magnesium ion. The QM/MM-GBSA parameters are set as follows:
&general
startframe=1, endframe=100, interval=5,
keep_files=0,verbose=1,search_path=1,
receptor_mask=":1-916:918", ligand_mask=":917:919"
/
#&pb
#istrng=0.1,
#
&gb
saltcon=0.1,ifqnt=1,qmcharge_com=0,qmcharge_rec=2,
qmcharge_lig=-2,qm_theory='PM3',qm_residues="917-919",
/
1-916 is protein, 917 and 918 are two Magnesium ions, and 919 is ATP.
The binding free energy has a large fluctuation, and some part of energy output results is shown:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
EGB -910.8454 711.7355 159.1489
ESCF 199.0339 829.5371 185.4901
DELTA G gas 607.9983 5.3856 1.2043
DELTA G solv -917.4764 711.7595 159.1543
DELTA TOTAL -110.4443 135.1893 30.2292
Is there any wrong parameter setting in my input file for QM/MM-GBSA method? Would you like to give me some suggestions about this or QM/MM-GBSA calculation? Thank you!
Best wishes
Duan Baogen
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Received on Thu Apr 11 2013 - 05:30:02 PDT
