Hi Elvis!
Yes! the above was a typo error! sorry.
I changed the 'indiel' parameter and I was finally able to correct the
error.
Thank you very much for all the help!
El vie., 28 ago. 2020 a las 0:28, Elvis Martis (<elvis_bcp.elvismartis.in>)
escribió:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Camila*
_______________________________________________
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Received on Fri Aug 28 2020 - 16:00:02 PDT
