Re: [AMBER] MMPBSA problem

From: Bill Miller III via AMBER <>
Date: Tue, 28 Feb 2023 11:41:53 -0600

I would definitely suggest using to generate your prmtop
files for

Looking at your tleap input file, all your prmtop files (complex, receptor,
and ligand) all come from different PDBs so there is no guaranteed
consistency between them. Using correctly will help with
that. But without knowing the details of what is in your cpx_w.prmtop file,
it's difficult to suggest what the problem would be with your command. One common issue users have is when they have more
than one ligand residue in the complex. So if your LIG/KOR residue is bound
to your complex in multiple places, that would confuse's initial guess and would require more user input from you,
but can still be done correctly by following the syntax for using

Hope that helps.

On Tue, Feb 28, 2023 at 9:52 AM Jurica Novak via AMBER <>

> 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
> quit
> 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.
> Jurica
> ________________________________
> 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?
> ....dac
> _______________________________________________
> AMBER mailing list

Bill Miller III
Assistant Professor of Chemistry
Truman State University
AMBER mailing list
Received on Tue Feb 28 2023 - 10:00:03 PST
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