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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Received on Fri Mar 29 2019 - 23:00:02 PDT
