*Dear Amber Experts,*
I am running MD simulation for a protein ligand complex to determine
selectivity. When I calculate the binding free energy, the MMGBS value is
according to the published data. But when I perform energy decomposition
using MMGBSA.py (Amber Tools 13) to calculate per residue contribution, all
of the energy shift difference shifts toward ligand, and the contribution
of amino acids become opposite.
I am using following input command for MMGBSA and decomposition. Please
check it weather there is some problem in my input command or I am missing
something. Or please if possible send me input command files for MMGBSA,
and Decomposition. Mine are given below:
*MMGBSA.in*
Input file for running PB and GB
&general
verbose=1, interval=5,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+",
/
&gb
igb=5, saltcon=0.100
/
&pb
istrng=0.100,
/
..........................................................
*DECOMP.in*
Per-residue GB and PB decomposition
&general
verbose=1,
#search_path=1,
interval=10,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100, inp=1, radiopt=0,
/
&decomp
idecomp=1,
dec_verbose=3,
/
--
*Regards,*
*Tahir Ali Chohan*
*B.Pharm., M.Phil (Pharm. Chem.)*
*PhD Scholar*
*College of Pharmaceutical Sciences*
*Zhejiang University, Hangzhou, China.*
*Cell # 0086-13018996850*
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Received on Fri May 16 2014 - 12:30:02 PDT
