[AMBER] MMPBSA problem

From: Jurica Novak via AMBER <amber.ambermd.org>
Date: Fri, 24 Feb 2023 09:32:13 +0000

Dear Amber Users,

I am having trouble identifying the source of error in the MMPBSA.py calculation.
1 us MD simulation ends normally, and when I visualize the trajectory, everything seems fine. After running the MMPBSA.py calculation
MMPBSA.py -O -i mmpbsa.in -o res_deltaG_01.dat -do decomp_01.dat -sp cpx_w.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y md_01.mdcrd
I received the message Fatal Error! In the file _MMPBSA_complex_gb.mdout.0 I found the cause of the error: FATAL: NATOM mismatch in coord and topology files I checked all prmtop files - complex in water (16703 residues, 56217 atoms), complex (470, 7760), receptor (469,7705) and ligand (1, 55), and the numbers match the number of atoms in the original pdb file.
For some reason, the files generated by MMPBSA.py do not have the correct number of atoms - _MMPBSA_complex.pdb, _MMPBSA_receptor.pdb, and _MMPBSA_ligand.pdb are the same files, all containing only the receptor.
I used the same protocol and scripts to generate files for four different ligands. Only in one case the calculation with MMPBS.py finished normally, while in the other cases I got the same fatal error.

Please help me to solve the MMPBSA problem. If necessary, I can provide all the files.

Best regards,

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Received on Fri Feb 24 2023 - 02:00:02 PST
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