Hi Abhilash,
Thank you very much for the reply. I think -s -n -r options of
antechamber.py allow users to strip the mask for the
lignad or the receptors. One can define the similar thing in the input file
of MMGB(PB)SA by ligand_mask or receptor_mask.
So, either of the way in my case would be
:26-50,:51-75,:76-100,:101-125,:126-150. Here, the residues belonging to
the masks
are five separate ligands that are supposed to bind one after another to
form the complex.
However, I am not sure whether such masking will treat those five ligands
as separate ligands i.e., the interaction between them
will be considered so that contribution out of it will be reflected in the
total binding free energy. My experience is that such masking
treat all the ligands together a single ligand and thus probably their
inter-ligand contribution is not accounted in the total binding free
energy. Please let me know how to take care that. I assume you had the
similar case i.e., you also had to treat the ligands separately so that
inter-ligand contribution is also accounted.
Sincerely,
Prabir
On Sat, Mar 30, 2019 at 3:43 AM Abhilash J <md.scfbio.gmail.com> wrote:
> 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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> > >
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> >
> _______________________________________________
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>
--
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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Received on Sat Mar 30 2019 - 10:00:03 PDT
