Hi,
I am running MMPBSA simulations with the LRH-1 receptor and a ligand. I have made files for the complex of the two, the receptor alone, the ligand. I have no problem running the simulation, but then when I get to the analysis, I use the analysis script that is on amber tutorials website. However, the files run until the _MMPSA_complex_gb.mdout.0 file and within the nohup file I have this error:
Beginning GB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
calculating complex contribution...
File "/usr/local/amber20/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py", line 156, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /usr/local/amber20/bin/mmpbsa_py_energy failed with prmtop com.top!
Exiting. All files have been retained.
Within the _MMPSA_complex_gb.mdout.0 file, I have these errors:
Processing frame 5
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2675) enb14 --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2676) eel14 --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2734) enb --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2735) eel --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2736) e_gb --> nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2737) esurf --> 0.000
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2738) evdwnp --> 0.000
BOND = -nan ANGLE = -nan DIHED = -nan
VDWAALS = -nan EEL = -nan EGB = nan
1-4 VDW = -nan 1-4 EEL = -nan RESTRAINT = 0.0000
ESURF = 0.0000
Processing frame 6
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2675) enb14 --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2676) eel14 --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2734) enb --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2735) eel --> -nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2736) e_gb --> nan
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2737) esurf --> 0.000
/usr/local/amber20_src/AmberTools/src/sff/eff.c(2738) evdwnp --> 0.000
BOND = -nan ANGLE = -nan DIHED = -nan
VDWAALS = -nan EEL = -nan EG
I have been looking through the amber archives for an answer on how to fix this but I have been unable to find an answer.
Thank you, and hope to hear from you soon,
Sarah Abraham
Emory 23' Biology B.S | Chemistry B.A
Student Researcher Ortlund Lab
Scribe Emory University Hospital
Sarah Abraham
Emory 23' Biology B.S | Chemistry B.A
Student Researcher Ortlund Lab
Scribe Emory University Hospital
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Received on Thu Apr 06 2023 - 06:30:02 PDT
