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From: Camila Clemente <camilamaraclemente.gmail.com>

Date: Fri, 28 Aug 2020 19:41:09 -0300

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>)

escribiÃ³:

*> 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
*

*> > >)
*

*> > escribiÃ³:
*

*> >
*

*> > > 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
*

*>
*

Date: Fri, 28 Aug 2020 19:41:09 -0300

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>)

escribiÃ³:

-- *Camila* _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Aug 28 2020 - 16:00:02 PDT

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