Thank you so much for the instant help.. I put the suggested value in my input file ( inp=1, radiopt=0 ). Now it end with some warning message. but these warning message are just informational messgaes.
Now My input file is..
Input file for running PB and GB in serial
&general
endframe=50, keep_files=2,
strip_mask=":WAT,CL-,Na+",
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100, inp=1, radiopt=0
/
-----Original Messages-----
From: "Ñî´¨" <junaid.hust.edu.cn>
Sent Time: Monday, September 21, 2015
To: amber.ambermd.org
Cc:
Subject: Problem In Performing MMPBSA Calculation for System containing Ligand and Protein
Dear Amber Users
I have simulated the complex using amber14 with GPU. I have got problem while running the MMPBSA.py . I have got this problem with several complexes.
I used this commond
MMPBSA.py -O -i mmpbsa_2b.in -o final.dat -sp com_solvated.top -cp com.top -rp rec.top -lp lig.top -y *.mdcrd
My input file is..
Input file for running PB and GB in serial
&general
endframe=50, keep_files=2,
strip_mask=":WAT:CL-"Na+",
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
the error message said.....
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber14/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber14/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /opt/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /opt/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
File "/opt/amber14/bin/MMPBSA.py", line 104, in <module>
app.run_mmpbsa()
File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 416, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber14/bin/mmpbsa_py_energy failed with prmtop com.top!
PB Bomb in pb_aaradi(): No radius assigned for atom 11 CB 2C
Exiting. All files have been retained
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Received on Mon Sep 21 2015 - 19:30:03 PDT
