You should be able to do this entire process using only ante-MMPBSA.py.
ante-MMPBSA.py is essentially a user-friendly way of running parmed to make
prmtop files for MMPBSA.py. If I understand your system correctly, this
should work:
ante-MMPBSA.py -p complex_solvated.prmtop -c complex.prmtop -r
receptor.prmtop -l ligand.prmtop -s :WAT:Cl-:Na+:348:349 -n :378
The -s flag tells ante-MMPBSA.py what your solvent is that you want
completely removed from all calculations (so in this case, water, chloride
ions, sodium ions, and ions corresponding to residues 348 and 349). So if
you have other ions in your system, you should add them here. You can also
replace ":348:349" with simply the residue name for your ions that are
residues 348 and 349.
The -n flag tells MMPBSA.py with residue(s) you want to be considered the
ligand from what is left after removing all the solvent/ions. In this case,
the incoming nucleotide residue 378 is being considered the ligand. You can
also use its 3-4 letter residue name in place of the residue number if the
name is unique and not present elsewhere in your system.
This command will make your dry complex.prmtop, receptor.prmtop, and
ligand.prmtop files prepped for MMPBSA.py. One other note is that
ante-MMPBSA.py will not overwrite files, so if complex.prmtop,
receptor.prmtop, or ligand.prmtop
If this doesn't work, feel free to send me the prmtop off list and I can
figure out a command that will work for you.
-Bill
On Thu, Dec 18, 2025 at 2:54 AM Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> Kindly suggest some ways to rectify this.
>
> On 2025-12-15 19:29, Priyasha Majee wrote:
>
> > Hello All,
> >
> > I am trying to do MMPBSA. My system is a complex of protein and DNA
> > system with an incoming nucleotide. I want to see the binding affinity
> > of nucleotide with DNA template in wild type and mutant protein-DNA
> > system. My system has 1-347 amino acids, 348-349 ions and 350-377 DNA
> > (both template and complementary ssDNA) and 378 as the incoming
> > nucleotide. The system parameter file is nowation.prmtop which doesn't
> > have water and Na+ ions. The corresponding trajectory is comp.nc. I
> > tried to generate the complex, receptor and ligand .prmtop file using
> > parmed. For complex I used:
> >
> > cp nowation.prmtop complex.prmtop
> >
> > For ligand
> >
> > Parmed nowation.prmtop
> >
> > Strip ! (:378)
> >
> > Outparm ligand.prmtop
> >
> > For Receptor
> >
> > Parmed nowation.prmtop
> >
> > Strip :'348-349, 378'
> >
> > Outparm receptor.prmtop
> >
> > The trajectory I am using the original trajectory stripped off water
> > and ions.
> >
> > When I am trying to run the MMPBSA job,
> >
> > It is showing complex.prmtom != receptor.prmtop + ligand.prmtop.
> >
> > Kindly please suggest where am I going wrong?
> >
> > Thank you
> >
> > Regards
> >
> > Priyasha
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>
--
Bill Miller III
Associate Professor of Biochemistry
A.T. Still University
417-549-0952
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Received on Thu Dec 18 2025 - 08:00:02 PST
