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*
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Received on Thu Aug 27 2020 - 10:30:04 PDT
