Dear Dac
Thank you very much for your reply.
I tried one of the state as below:-
"A" "B"
Protein+cofactor1+cofactor2 ligand
both of the cofactors are the same but bind at the different binding sites.
Is it the correct way?
I am getting the error with ligand prmtop as mentioned below:-
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp complex.prmtop
-cp complexdry.prmtop -rp protein_cofactordry.prmtop -lp G6P_n.prmtop -y
Prod.crd
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/rcms/Downloads/Amber/amber20/bin/cpptraj
mmpbsa_py_energy found! Using
/home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
Preparing trajectories for simulation...
2000 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/home/rcms/Downloads/Amber/amber20/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
File "/home/rcms/Downloads/Amber/amber20/bin/MMPBSA.py", line 100, in
<module>
app.run_mmpbsa()
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/rcms/Downloads/Amber/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 475, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /home/rcms/Downloads/Amber/amber20/bin/cpptraj failed with
prmtop G6P_n.prmtop!
Exiting. All files have been retained.
Could you please suggest to me where I am doing mistake?
Thanks in advance.
Sadaf
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On Sun, 17 Jan 2021 at 20:17, David A Case <david.case.rutgers.edu> wrote:
> On Sun, Jan 17, 2021, Sadaf Rani wrote:
>
> >I have a query and need your suggestions, please. I want to calculate
> >ligand binding affinities of a protein-ligand complex in which I have 1
> >ligand and two cofacors in the same complex. How should I calculate
> binding
> >affinities of all with protein using mmpbsa? Do I need to built separate
> >complexes for all of the three ligands (ligand plus cofactors)?
>
> Don't be confused by the terms "protein", "ligand" and "complex". MMPBSA
> doesn't know any chemistry, it effectively always treats a two-component
> system, A + B -> C, where A, B and C can be anything you want.
>
> To describe the binding of three components, you could do some combination
> of the following calculations, depending on what information you wish to
> obtain; (in this table, "C" would alway be the combination of "A" and "B"):
>
> "A" "B"
> ----------------------------------------------
> 1. protein ligand
> 2. protein+ligand cofactor1
> 3. protein+ligand+cofactor1 cofactor2
> 4. protein+cofactor1 ligand
>
> ....etc...etc. The order of the calculations doesn't matter, at least
> in principle. And you probably don't need all the steps. With a protein
> plus three binders, there are *many* possible states, depending on whether
> each binder has its own pocket (and so can only bind in one place), and
> whether the two cofactors are the same or different. If each binder can
> only bind in its "own" pocket, you would have
>
> nothing bound 1 state
> 1 item bound 3 states
> 2 items bound 3 states
> 3 items bound 1 state
>
> But is is very rare that you would want to simulate all of them.
>
> ...hope this helps....dac
>
>
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Received on Tue Jan 19 2021 - 23:00:02 PST
