Thank you Jason,
The objective of my simulation is to determine whether a particular compound (DEET) result in an increase of the binding energy of the two subunits of a homodimer. Part of DEET is extending into the interface of the two subunits of the homodimer.
Answering your question
> On 23 Mar 2016, at 02:45, Jason Swails <jason.swails.gmail.com> wrote:
> It's unclear to me what you are defining as your "ligand". Is the water
> included in your receptor or ligand topology?
>
Topology of Receptor = subunit_A + DEET + water
Topology of Ligand = subunit_B + DEET + water
> An extra water molecule can
> make a fairly substantial difference in calculated binding energies using
> MM/PBSA or MM/GBSA. Both due to polar and nonpolar solvation
> contributions. Particularly if the water molecule is "floating out in
> space" in some of the frames. (It's not clear what you mean by "does not
> exchange", but only "85% occupancy"…)
Point taken. What I meant is that the water molecule forms bridged h-bonds with DEET and specific residues both subunits for ~85% of the trajectory time.
What surprised me is the big drop in the energy of binding of the two subunits that was observed after stripping the water molecules from the trajectory. I cannot explain how stripping the water molecule can have such as large effect on the binding of the two subunits particularly as the water molecules are not in contact with any of the protein interface residues.
Thank you once again for your attention
George
>
>
> On Mon, Mar 21, 2016 at 1:05 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I’ve been trying to work out the binding energy of a homodimer, with 2
>> ligands and 2 water molecules (one per subunit).
>>
>> I’ve generated two independent 100 ns trajectories.
>>
>> I calculated the binding energy using the following input script
>>
>> Input file for running PB and GB
>> &general
>> strip_mask = :WAT,Na+,&!:271-272
>> endframe=10000, verbose=1, interval=20,
>> # entropy=1,
>> /
>> &gb
>> igb=2, saltcon=0.100
>> /
>> &decomp
>> idecomp=1,
>> dec_verbose=1,
>> /
>>
>> 271 and 272 are the said two water molecules. They do not exchange with
>> bulk solvent (occupancies > 85%)
>>
>> In both cases mmpbsa.py.MPI through WARNINGS
>>
>> GENERALIZED BORN:
>>
>> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
>> TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
>>
>> the origin of these warning as it has been discussed previously in the
>> list and my understanding is that they are not deemed important for single
>> trajectories.
>>
>> Differences (Complex - Receptor - Ligand)
>> DIHED 0.0001 0.0054
>> 0.0002
>> DIHED 0.0000 0.0056
>> 0.0003
>> (For BOND and ANGLE) the corresponding differences are zero.
>>
>
> These are *tiny* differences. It wouldn't surprise me if there was some
> kind of difference in improper torsion ordering between the bound and
> unbound states. That's really the only thing that makes sense here, and I
> know that, while uncommon, it *does* happen. I think it's important when
> potential problems are flagged and brought to your attention (which is why
> MMPBSA.py warns in cases like these), but in this instance I think the
> warning is benign.
>
>
>> BINDING ENERGY RESULTS OBTAINED
>>
>> For trajectory 1, the binding energy = -54 kcal/mol
>> For trajectory 2, the binding energy = -47 kcal/mol
>>
>> I stripped the water molecules and generated new topologies with
>> ante-mmpbsa.py
>> I run mmpbsa.py using the same script as above with the only difference
>> that the strip_mask was quoted out.
>>
>> For trajectory 1, the binding energy = -49 kcal/mol
>> For trajectory 2, the binding energy = -37 kcal/mol
>>
>> I don’t think these discrepancies are due to the water molecules, (1)
>> because they are not at the binding interface although they do form h-bonds
>> with the ligands part of which is at the binding interface and (2) because
>> mmpbsa-decomp gives
>> for water1 -0.14 kcal/mol (trajectory 1); -0.22 kcal/mol (trajectory 2) &
>> for water2 —0.03 kcal/mol (trajectory 1); -0.11 kcal/mol (trajectory 2)
>>
>> I’d appreciate any suggestions explaining this behaviour.
>>
>
> It's unclear to me what you are defining as your "ligand". Is the water
> included in your receptor or ligand topology? An extra water molecule can
> make a fairly substantial difference in calculated binding energies using
> MM/PBSA or MM/GBSA. Both due to polar and nonpolar solvation
> contributions. Particularly if the water molecule is "floating out in
> space" in some of the frames. (It's not clear what you mean by "does not
> exchange", but only "85% occupancy"...)
>
> At the end of the day, MM-PBSA and MM-GBSA are very simple analyses, which
> limits the possible explanations that can exist for the behavior you're
> seeing.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Wed Mar 23 2016 - 06:00:07 PDT
