Jurica,
Using your cpx_w.prmtop, I ran the following command:
$AMBERHOME/bin/ante-MMPBSA.py -p cpx_w.prmtop -c complex.prmtop -r
receptor.prmtop -l ligand.prmtop -s :WAT:Cl-:Na+ -n :KOR
And received complex, receptor, and ligand prmtop output files that appear
correct.
The complex prmtop has all amino acids, the heme group, and the KOR ligand.
7760 atoms.
The receptor prmtop only has amino acids and the heme group. 7705 atoms.
And the ligand prmtop only has the KOR ligand. 55 atoms.
7705 + 55 atoms = 7760 atoms
So that command should work for you.
-Bill
On Wed, Mar 1, 2023 at 3:25 AM Jurica Novak <jurica.novak.biotech.uniri.hr>
wrote:
> Dear Prof. Miller,
>
> Running MMPBSA calculation using prmtop files generated by ante-MMPBSA.py
> resulted with the same error. I'm attaching cpx_w.prmtop and trajectory
> with 2 MD steps.
>
> Jurica
> ------------------------------
> *From:* Bill Miller III <brmilleriii.gmail.com>
> *Sent:* Tuesday, February 28, 2023 6:41 PM
> *To:* Jurica Novak <jurica.novak.biotech.uniri.hr>; AMBER Mailing List <
> amber.ambermd.org>
> *Cc:* David A Case <david.case.rutgers.edu>
> *Subject:* Re: [AMBER] MMPBSA problem
>
> I would definitely suggest using ante-MMPBSA.py to generate your prmtop
> files for MMPBSA.py.
>
> 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 ante-MMPBSA.py 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 ante-MMPBSA.py 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
> ante-MMPBSA.py's initial guess and would require more user input from you,
> but can still be done correctly by following the syntax for using
> ante-MMPBSA.py.
>
> Hope that helps.
> -Bill
>
> On Tue, Feb 28, 2023 at 9:52 AM Jurica Novak via AMBER <amber.ambermd.org>
> wrote:
>
> Dear prof. Case,
>
> No, I did not use ante-MMPBSA.py, 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 ante-MMPBSA.py, but when I run MMPBSA.py,
> 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 <david.case.rutgers.edu>
> Sent: Tuesday, February 28, 2023 2:42 PM
> To: Jurica Novak <jurica.novak.biotech.uniri.hr>; AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] MMPBSA problem
>
> On Fri, Feb 24, 2023, Jurica Novak via AMBER wrote:
> >
> >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.
>
> Something must be going wrong at the preparation stage: did you use
> ante-MMPBSA.py? 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
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Bill Miller III
> Assistant Professor of Chemistry
> Truman State University
> 417-549-0952
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Wed Mar 01 2023 - 08:00:03 PST
