[AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)

From: Nada Afiva <nadaafiva.gmail.com>
Date: Sun, 5 Jul 2020 04:58:44 +0700

Dear Amber list,
I was performing MMGBSA and MMPBSA binding energy calculations.
My system consisted of protein + DNA (555 residues), one Mn2+ ion, and
ligand, so the complex contains 557 residues.
I use NetCDF trajectory file after stripping out water, Na+, and Cl- ions
I obtained complex, receptor, and ligand topologies using ante-MMPBSA.

ante-MMPBSA.py -p complex01.prmtop -c complex.prmtop -s '!:1-557' -r
receptor.prmtop -m :1-556 -l ligand.prmtop

I used AmberTools16, but then I encountered the error below:
CalcError: /home/amber16/bin/cpptraj failed with prmtop file complex.prmtop!
Error occurred on rank 1.

Attached is my input file and output files.
I looked into _MMPBSA_complex_gb.mdout.1, but it said nothing about the

Command to perform mmgbsa and mmpbsa:
mpirun -np 2 MMPBSA.py.MPI -O -i mmpbsa1.in -cp complex.prmtop -rp
receptor.prmtop -lp ligand.prmtop -y nowat.prod.nc -o final.dat

If you have any suggestions, please help me.

Best regards,

AMBER mailing list

Received on Sat Jul 04 2020 - 15:00:02 PDT
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