Hi,
I used Quasi-harmonic approximation for entropy calculation and it did
not give me any standard deviation (SD).
The heads are divided into Translational, Rotational, Vibrational and
Total for each of complex, receptor and ligand.
I think it does is relevant for enthapic calculations and not overlapping
in this case.
Regards
On Wed, Jun 14, 2017 at 8:55 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> HI,
>
> it would be good to put your SD values. This SD will tell you how
> significantly different are your values for MD1 and MD2.
>
> For example.
>
> The entropy value for MD1= -36.56 and for MD2= - 38.42, lets say the SD
> for MD1 = 2 and for MD3 = 3, then these values are not significantly
> different because with uncertainty considered both systems will have
> overlapping values. Similarly, will be the case with the enthapy values.
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
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> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Abhilash J <md.scfbio.gmail.com>
> Sent: 14 June 2017 17:12:23
> To: AMBER Mailing List
> Subject: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis
>
> Hi everyone,
>
> I am doing MMGBSA and RMSF analysis of binding of two ligands (ligand1
> and ligand2) to a protein at 2 sites (site 1 and site 2).
> The idea is to see the effect replacement of one ligand (say ligand1) at
> site 1 with ligand2 to the binding of ligand1 at site2.
> So i ran two MDs (MD1 and MD2).
> First one consisted of ligand1 at both sites and the second having
> ligand2 at site1 and ligand1 at site 2.
> I ran the system for 350ns.
> After MMGBSA i found there is decrease in affinity of ligand1 to site 2
> upon replacement of ligand1 with ligand2 at site1.
>
> the enthalpic and entropic contributions at site 2 changed as follows (the
> ligand at this site has remained same, changes are due to replacement of
> ligand at the other site)
> MD1 MD2
> Enthalpic -45.51 --> -43.84
> Entropic(TDeltaS) -36.56 --> -38.42
> Total -8.95 --> -5.43 kcal/mol
>
> The enthalpic term is ok as it is increasing hence the decrease in final
> binding affinity.
> Issue is with entrpoic term.
> From RMSF analysis of protein i know there is increase in RMSD of almost
> every residue in the protein (including active site residues) hence i
> believe there is increase in entropy overall.
> It also seems ok to think this increase in entropy will lead to decrease
> in binding affinity.
> But entropic value in MM GBSA analysis goes from -36.56 to -38.42 i.e. a
> net decrease in value. Does this mean entropy is decreasing according to
> MMGBSA?
> Or does increase in entropy lead to a more negative value of TDeltaS?
> I am a bit confused. I am ready to elaborate if the question is not
> clear.
>
> Regards
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Received on Wed Jun 14 2017 - 09:30:02 PDT
