Hello, everyone,
I'm learning MMPBSA.py recently, for the sake of calculating the
binding free energy of protein with an organic molecule. Though
AmberTools13 Reference Manual, to make the calculation more accurate, I
choose INP=2 (which is default, and I have use -make-mdins option to
check the temporary mdin files) to decompose non-polar solvation energy
into cavity and dispersion terms. In the meanwhile, I need to set
radiopt=1. My input file is written as:
Input file for running PB and GB
&general
startframe=0, endframe=600, interval=10,
verbose =2,
# entropy =1,
strip_mask=:WAT:Na+
/
&gb
igb=5, saltcon=0.100
/
&pb
radiopt=1,
istrng=0.100,
indi =1,
/
and I get the error information as:
CalcError: /gpfs01/home/ymei/software/amber14/bin/mmpbsa_py_energy
failed with prmtop com_nobox.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB
2C
Exiting. All files have been retained.
In addition, I did a test, no matter the ligand is a protein or an
organic molecule, and both in MMPBSA.py and mm_pbsa.pl, this error will
occur. Can anyone tell me what this error information stand for and how
to use radiopt = 1 correctly?
I would be appreciate for the helps!
Sincerely yours,
Wei Liu，
wliu.itcs.ecnu.edu.cn
East China Normal University
ShangHai，china，200062
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Received on Tue Apr 21 2015 - 09:00:03 PDT
