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

From: Nada Afiva <>
Date: Sun, 5 Jul 2020 10:17:36 +0700

Dear list,
I am guessing the error was caused by Mn2+ ion.
I previously performed MD simulation with Mn2+ ion as part of receptor
along with DNA, and
I got netCDF file after stripping water, Na+ and Cl- ions.
Can I reorder the Mn2+ position in the trajectory file so that the ion is
placed after ligand.
I want to perform mmpbsa calculation after removing the Mn2+ along with
water, Na and Cl ions.
Please correct me if my understanding is wrong.
Thank you.
Best regards,

Pada tanggal Min, 5 Jul 2020 pukul 04.58 Nada Afiva <>

> 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.
> -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
> error.
> Command to perform mmgbsa and mmpbsa:
> mpirun -np 2 -O -i -cp complex.prmtop -rp
> receptor.prmtop -lp ligand.prmtop -y -o final.dat
> If you have any suggestions, please help me.
> Best regards,
> Nadaafiva
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Received on Sat Jul 04 2020 - 20:30:02 PDT
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