Gabriela Lima
Hello, I'm trying to perform a QM/MM calculation with a protein-ligand complex, but I'm dealing with the following error:
[INFO ] calculating complex contribution... 0%| | 0/1001 [elapsed: 00:00 remaining: ?] File "/home/gabrielalima/anaconda3/envs/mmpbsa/bin/gmx_MMPBSA", line 8, in <module> sys.exit(gmxmmpbsa()) File "/home/gabrielalima/anaconda3/envs/mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa app.run_mmpbsa() File "/home/gabrielalima/anaconda3/envs/mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 203, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/home/gabrielalima/anaconda3/envs/mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 131, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/home/gabrielalima/anaconda3/envs/mmpbsa/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 208, in run raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!') CalcError: /home/gabrielalima/Downloads/amber20/bin/sander failed with prmtop COM.prmtop! Exiting. All files have been retained.
I have already performed the structure fit, removed the PBC, but it still hasn't solved the issue. The same input file with another complex worked perfectly.
The command I am using is:
gmx_MMPBSA -O -i ../../qmmm.in -cs 6_md.tpr -ci index.ndx -cg 1 13 -ct 6_md_fit.xtc -cp topol.top -nogui -o results.dat -eo results.csv
What could be wrong? I am sending the files attached and the trajectory file can be obtained here (https://drive.google.com/file/d/1lH8IUwa0NRyGapyzy5UANsWohYV2JSgT/view?usp=sharing).
Thank you in advance.
