Dear Amber users,
I am trying to run MMPBSA for my complex (protein + peptide-sugar structure). My input file is:
Sample input file for GB and PB calculation
&general
startframe=1, endframe=1000, interval=20,
verbose=2, debug_printlevel=2, strip_mask=:WAT,Na+
/
&gb
igb=2, saltcon=0.150,
/
&pb
istrng=0.15, fillratio=4.0
/
MMPBSA_py command:
MMPBSA.py -O -i mmpbsa_py.in -o MMPBSA_PB-GB.txt -sp COM_solvated.prmtop -cp COM.prmtop -rp REC.prmtop -lp LIG.prmtop -y *.mdcrd
For prmtop files preparation I used GLYCAM_06h ff. During BFE calculations I am getting an error:
File "/lap/amber/12.0.13/bin/MMPBSA.py", line 565, in <module>
external_progs, '_MMPBSA_', normal_system)
File "/afs/hpc2n.umu.se/lap/amber/12.0.13/amd64_ubuntu1004/bin/MMPBSA_mods/calculation.py", line 176, in run_calculations
calc.Run()
File "/afs/hpc2n.umu.se/lap/amber/12.0.13/amd64_ubuntu1004/bin/MMPBSA_mods/calculation.py", line 665, in Run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /lap/amber/12.0.13/bin/mmpbsa_py_energy failed with prmtop COM.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 93 O1 Os
Exiting. All files have been retained.
How could I avoid this error? Thank you in advance for your help.
best regards
/Urszula
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Received on Sun May 12 2013 - 23:30:02 PDT
