On Mon, Sep 21, 2015 at 12:30 AM, 杨川 <junaid.hust.edu.cn> wrote:
> 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
>
If you Google this error message, you will find that the suggested fix is
to set inp=1 and radiopt=0 in the &pb section.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 04:30:04 PDT
