Re: [AMBER] Problem with mmpbsa

From: Elvis Martis <>
Date: Mon, 20 Feb 2017 12:15:15 +0000

Have you set the environments correctly?
Try to run this command before running mmpbsa
Source $AMBERHOME/ (bash)
Source $AMBERHOME/amber.csh (csh)

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Tiffani Rovira []
Sent: Monday, February 20, 2017 5:41 PM
Subject: [AMBER] Problem with mmpbsa

Hi users,

I have the following problem with the mmpbsa calculation:

Loading and checking parameter files for compatibility...
  File "/opt/amber16/bin/", line 98, in <module>
  File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 572, in loadcheck_prmtops
    FILES.receptor_prmtop, FILES.ligand_prmtop)
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 109, in __init__
"/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/", line 876, in _validate
    raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom Exiting. All files have been retained.

I already have tried to solve it but I couldn't.

How can deal with this problem?


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