Re: [AMBER] MMPBSA problem

From: Jurica Novak via AMBER <>
Date: Tue, 28 Feb 2023 15:52:10 +0000

Dear prof. Case,

No, I did not use, all prmtop files were generated with tleap:
source leaprc.protein.ff19SB
source leaprc.gaff
#loadamberparams frcmod.ionsjc_tip3p
source leaprc.water.tip3p
loadOff atomic_ions.lib
# load frcmod
loadamberparams kortikosteron.frcmod
loadamberparams hem_SI.frcmod
loadamberparams cyp_SI.frcmod
# load lib
loadoff hem_SI.lib
loadoff cyp_SI.lib
loadoff kortikosteron.lib
# load ligand
KOR = loadmol2 kortikosteron.mol2
LIG = loadpdb kortikosteron.pdb
check LIG
saveoff LIG kortikosteron.lib
saveamberparm LIG ligand.prmtop ligand.inpcrd
# load receptor
REC = loadpdb receptor.pdb
bond REC.441.C REC.442.N
bond REC.442.C REC.443.N
check REC
saveamberparm REC receptor.prmtop receptor.inpcrd
# load complex
CPX = loadpdb complex.pdb
bond CPX.441.C CPX.442.N
bond CPX.442.C CPX.443.N
check CPX
saveamberparm CPX complex.prmtop complex.inpcrd
savepdb CPX cpx.pdb
# neutralization & solvation
addIons CPX Cl- 0
solvateoct CPX TIP3PBOX 12
addIonsRand CPX Na+ 58 Cl- 58
saveamberparm CPX cpx_w.prmtop cpx_w.rst
savepdb CPX cpx_w.pdb

All loaded pdb files were generated from the original pdb of the complex by removing either the ligand or the receptor. Following your suggestion, I tried preparing prmtop files with, but when I run, I get the same error, again with the files MMPBSA_complex.pdb, _MMPBSA_receptor.pdb and _MMPBSA_ligand.pdb containing only the receptor.

In preparing the system with successful and unsuccessful MMPBSA calculations, I used the same tleap script, followed the same protocols, and used the same parameters in the dynamics. As expected, the receptor.prmtop file is the same. The only difference between the systems is the number of atoms of the ligand.


From: David A Case <>
Sent: Tuesday, February 28, 2023 2:42 PM
To: Jurica Novak <>; AMBER Mailing List <>
Subject: Re: [AMBER] MMPBSA problem

On Fri, Feb 24, 2023, Jurica Novak via AMBER wrote:
>For some reason, the files generated by 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.

Something must be going wrong at the preparation stage: did you use This script tries to guess what the ligand and receptor
are, but is not foolproof. You may need to generate the prmtop/inpcrd files
by hand. Or at least, provide info about how you carried out the
preparation steps, in case some operator error is involved. Is there
anything different about the systems that worked OK and those that failed,
especially in regards to how clear it is what is the receptor and what is
the ligand?


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Received on Tue Feb 28 2023 - 08:00:02 PST
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