Dear Amber Users,
I have simulated a peptide in explicit solvent environment and saved the
trajectory. Now I am interested in doing stability calculation and for this
I am using MMPBSA.py.
As I have only a solvated prmtop file, I stripped solvent information and
created a prmtop file using following command.
*ante-MMPBSA.py -p wt_box.prmtop -c dry_wt_box.prmtop -s :19-652*5
Next I proceeded for stability calculation using both GB and PB models
using following command.
*MMPBSA.py -O -i mmpbsa.in <
http://mmpbsa.in> -sp wt_box.prmtop -cp
dry_wt_box.prmtop -y mdproduction1_wt_box.mdcrd*
Stability calculation using GB model finished successfully but the
calculation failed when I am using PB model.
*The error message I got:------------------------------------*Loading and
checking parameter files for compatibility...
mmpbsa_py_energy found! Using /home/saikat/ambertools14/bin/mmpbsa_py_energy
cpptraj found! Using /home/saikat/ambertools14/bin/cpptraj
Preparing trajectories for simulation...
20 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with
/home/saikat/ambertools14/bin/mmpbsa_py_energy
calculating complex contribution...
File "/home/saikat/ambertools14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/home/saikat/ambertools14/bin/MMPBSA_mods/main.py", line 218, in
run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/saikat/ambertools14/bin/MMPBSA_mods/calculation.py", line 79,
in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/saikat/ambertools14/bin/MMPBSA_mods/calculation.py", line
416, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/saikat/ambertools14/bin/mmpbsa_py_energy failed with
prmtop dry_wt_box.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 171 CG C6
Exiting. All files have been retained.
*------------------------------------*
Could anyone suggest why I am not able to use PB model for the calculation.
With warm regards,
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
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Received on Fri Jan 22 2016 - 02:30:03 PST
