Dear AMBER users,
I am using MMPBSA.py to calculate the binding free energy between two
protein chains. I have tried both GB and PB calculations (input file is
copied here). However I get some warnings before the calculation is
complete(copied below). Is this something I have to worry about?
thanks in advanced,
*warnings:*
Running calculations on normal system...
Beginning GB calculations with
/home/ali/Downloads/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with
/home/ali/Downloads/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
*Input file:*
Input file for running PB and GB
&general
endframe=100, verbose=1,
# entropy=1,
/
&gb
igb=2, saltcon=0.00
/
&pb
istrng=0.00,
inp=1,
radiopt=0
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Received on Sat Oct 06 2018 - 00:30:03 PDT
