Hi,
I am not an expert with MMGB/PBSA but I working sometime back on a
single protein binding to multiple ligands simultaneously.
Your case seems slightly different. But the following might help.
You can define complex.prmtop drug.prmtop etc... using residue numbers
in ante-MMPBSA.py.
Look for -s and -m options in ante-MMPBSA.py part of AMBER manual.
For example:
python $AMBERHOME/ante-MMPBSA.py -p complex_wat.prmtop -c complex.prmtop
-r protein.prmtop -l drg.top -s '!(:1-589)' -m '!(:586)'
Here, residues 1-589 form the complex.
and residue 586 is the ligand. In Your case it might be residues 400-450
as your ligand is a protein in itself.
You can define your complex, receptor and ligand based on residue
numbers in your topology.
I am bit confused with your statement " I want to define one monomer as
receptor and rest of the five monomers as five ligands". I presume it is
other way round. Or i got this wrong.
Still, I hope it helps.
All the best.
Abhilash
On Sat, Mar 30, 2019 at 11:16 AM Prabir Khatua <prabir07chem.gmail.com>
wrote:
> Hi Elvis,
>
> I do not understand what want to mean by all the ligands bound to receptor
> simultaneously. I want to calculate binding free energy of a hexamer.
> However, I have simulated trajectory of the hexamer (complex in my case)
> only. Thus, I want to define one monomer as receptor and rest of the five
> monomers as five ligands considering the fact that the monomers bind one
> after another to form hexamer. Thus, the binding free energy that I am
> looking for should be
>
> Del G = G_hexa-G_mon1-G_mon2-G_mon3-G_mon4-G_mon5 -G_mon5
>
> However, I did not find a way to define multiple ligands and hence, I am
> not getting the right value of binding free energy as far as the process of
> hexamer formation is concerned. I hope I have made the problem clear to
> you. Please let me know if I answered your query and help me to sort
> out the problem.
>
> Thank you so much,
>
> Prabir
>
> On Fri, Mar 29, 2019 at 11:38 PM Elvis Martis <elvis.martis.bcp.edu.in>
> wrote:
>
> > HI,
> > Are all the ligands bound to the receptor simultaneously?
> >
> >
> > Best Regards
> >
> > Elvis Martis
> >
> >
> >
> > ________________________________
> > From: Prabir Khatua <prabir07chem.gmail.com>
> > Sent: 30 March 2019 02:44
> > To: AMBER Mailing List
> > Subject: [AMBER] MMPBSA
> >
> > Hello Amber Users,
> >
> > I want to calculate binding free energy of a complex having five
> identical
> > ligands. I really do not know how to define the ligand prmtop file in
> > MMPBSA.py.
> >
> > I tried something like
> >
> > mpirun -np 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmgbsa-1.in -o
> > SAA_2_hexa_104_S1_mmgbsa.dat -do SAA_2_hexa_104_S1_mmgbsa-decomp.dat -cp
> > com.prmtop -rp rec.prmtop -lp lig1.prmtop lig2.prmtop lig3.prmtop
> > lig4.prmtop lig5.prmtop -y SAA_2_hexa_104_S1.crd
> >
> > However, it is not working. Can anyone please suggest me how to use
> > multiple ligands in a single MMPBSA calculation? Any suggestion would be
> > appreciated.
> >
> > Thanks,
> >
> > Prabir
> >
> > --
> >
> > *Prabir Khatua*
> > *Postdoctoral Research Associate*
> > *Department of Chemistry & Biochemistry*
> > *University of Oklahoma*
> > *Norman, Oklahoma 73019*
> > *U. S. A.*
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> >
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Received on Sat Mar 30 2019 - 02:00:02 PDT
