Hi Camila
One thing strange I noticed in the VDWaals term for PBSA and GBSA, since
both are computed using MM, they should be identical. However, in your case
the magnitude is same but the signs are opposite, is this a typo??
Secondly, as I had mentioned earlier, PBSA results are also
Sensitive to internal dielectric (indiel) which depends on the binding
site. You would want to try this until right combination is obtained and
then comparing GBSA and PBSA can tell us of there are differences.
On Thursday, August 27, 2020, Camila Clemente <camilamaraclemente.gmail.com>
wrote:
> Hi Elvis,
>
> I attach a *short* analysis of MMPBSA.py where I show you the difference
> mentioned in the previous mail. It is important to note that it is a 0.5 M
> NaCl simulated protein.
>
> &general
> startframe=1, endframe=100, interval=5,
> verbose=2, keep_files=0,
> /
> &gb
> igb=8, saltcon=0.5,
> /
> &pb
> istrng=0.5, fillratio=4.0, inp=2,
> /
> ________________________________
> *GBSA*
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> ------------------------------------------------------------
> -------------------
> BOND 0.0000 0.0000
> 0.0000
> ANGLE -0.0000 0.0000
> 0.0000
> DIHED 0.0020 0.0134
> 0.0030
> VDWAALS 26.3194 1.9045 0.4259
> EEL -8.7449 5.2356
> 1.1707
> 1-4 VDW -0.0000 0.0000
> 0.0000
> 1-4 EEL -0.0000 0.0001
> 0.0000
> EGB 18.8887 3.2709
> 0.7314
> ESURF -3.5676 0.2215
> 0.0495
>
> DELTA G gas -35.0624 5.8176
> 1.3009
> DELTA G solv 15.3210 3.1379
> 0.7016
>
> DELTA TOTAL -19.7413 3.0275
> 0.6770
> __________
> *PBSA*
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> ------------------------------------------------------------
> -------------------
> BOND 0.0000 0.0000
> 0.0000
> ANGLE -0.0000 0.0000
> 0.0000
> DIHED 0.0020 0.0134
> 0.0030
> VDWAALS -26.3194 1.9045 0.4259
> EEL -8.7449 5.2356
> 1.1707
> 1-4 VDW -0.0000 0.0000
> 0.0000
> 1-4 EEL -0.0000 0.0001
> 0.0000
> EPB 18.2728 2.8427
> 0.6356
> ENPOLAR -20.4316 1.1227
> 0.2510
> EDISPER 34.8682 0.8758
> 0.1958
>
> DELTA G gas -35.0624 5.8176
> 1.3009
> DELTA G solv 32.7095 2.8180
> 0.6301
>
> DELTA TOTAL -2.3529 4.9661
> 1.1105
>
> What do you think could be happening?
> Thank you!
>
> El jue., 27 ago. 2020 a las 11:56, Elvis Martis (<elvis_bcp.elvismartis.in
> >)
> escribió:
>
> > Hi
> > In PBSA calculations, did you use inp=1 or 2. If left to default (inp=1),
> > try setting inp=2.
> > Also, PBSA calculations are sensitive to internal dielectric constant,
> > allowed values are 1 (non-polar binding site), 2 and 4 (polar binding
> > site).
> > You could experiment with these variations.
> >
> > On Thursday, August 27, 2020, Camila Clemente <
> > camilamaraclemente.gmail.com>
> > wrote:
> >
> > > Hi!
> > >
> > > I have made a simulation of a protein-ligand modifying the NaCl
> > > concentrations. The simulation with the highest salt concentration is
> > 0.5 M
> > > NaCl.
> > > I simulated 120 ns and I am doing the calculation of MMPBSA.py every 10
> > ns.
> > >
> > > When comparing the results of GBSA and PBSA, they are very different.
> The
> > > result for GBSA is very encouraging (-30kcal/mol) but the result for
> PBSA
> > > (1kcal/mol) is not.
> > > What could be the reason for such a difference in results between the
> two
> > > techniques? Is it the solvent system?
> > >
> > > Thank you for your help
> > > --
> > > *Camila*
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Best Regards
> > Elvis
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> *Camila*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis
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Received on Thu Aug 27 2020 - 20:30:02 PDT
