Hi there,
The problem was solved. It was my mistake to not set the radius (set default PBRadii mbondi2).
Thanks,Siavoush
On Wednesday, 15 March 2023 at 10:52:58 am GMT+3:30, Siavoush Dastmalchi via AMBER <amber.ambermd.org> wrote:
Dear List,
I am doing MMPBSA calculations on a ligand-receptor system following instruction provided in tutorial 3. After generating MD trajectories in production step (prod.mdcrd) I failed to run MMPBSA.py and am getting the following error messages:
$ MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com_solvated.prmtop -cp rec_7b.prmtop -rp rec.prmtop -lp lig.prmtop -y prod.mdcrd
Loading and checking parameter files for compatibility...
File "/opt/apps/amber14/bin/MMPBSA.py", line 94, in <module>
app.loadcheck_prmtops()
File "/opt/apps/amber14/bin/MMPBSA_mods/main.py", line 609, in loadcheck_prmtops
self.normal_system.CheckConsistency()
File "/opt/apps/amber14/bin/MMPBSA_mods/parm_setup.py", line 897, in CheckConsistency
raise PrmtopError('Topology files have inconsistent RADIUS_SETs')
PrmtopError: Topology files have inconsistent RADIUS_SETs
Exiting. All files have been retained.
I will appreciate it if I receive help on this.
Cheers,Siavoush
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Received on Wed Mar 15 2023 - 04:00:02 PDT
