Custom Search
-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Sep 21, 2015 at 7:15 PM, 杨川 <junaid.hust.edu.cn> wrote: > 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: "杨川" <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 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Sep 22 2015 - 11:30:03 PDT