Hi,
Thank you so much. I was exactly thinking to do it following the way you
mentioned. But, I was a bit worried about the conformational space.
Therefore, I was looking for an option, which could allow one to use a
single somulation. But, I think result that would be obtained using the
technique you mentioned would be okay in approximate sense if I am
interested to make a comparision.
Sincerely,
Prabir
On Sat, Mar 30, 2019 at 2:59 PM Wesley Michael Botello-Smith <
wmsmith.uci.edu> wrote:
> You could technically use the single trajectory mode as well, however, the
> underlying assumptions, namely that the conformatuonal space sampled by the
> receptor is the same in both bound and unbound state, may noy be valid here
>
> On Sat, Mar 30, 2019, 1:44 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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--
*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 - 16:30:03 PDT
