Difference between PBSA and GBSA

[Dong Man Jang]

Hello,

When I read article about MMGBSA, MMGBSA takes shorter time to calculate the binding free energy than MMPBSA, but both results for binding-free energy would be similar.

I downloaded examples from gmx_mmpbsa homepage and run gmx_mmpbsa (ST) after I add $pb lines in the file of mmpbsa.in like below,

---------------

 $ gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc -lm ligand.mol2

--------mmpbsa.in--------

&general

sys_name="Prot-Lig-ST",

startframe=5, endframe=20, verbose=2,

forcefields="oldff/leaprc.ff99SB,leaprc.gaff"

/

&gb

igb=5, saltcon=0.150,

/

&pb

istrng=0.15, fillratio=4.0

/

--------------------------

It gives the result as below,

GB model - Differences (complex - receptor - ligand)

DELTA TOTAL) -57.2477 

PB model - Differences (complex - receptor - ligand)

DELTA TOTAL) -2.53

I wonder if this is possible that both results show big differences.

I think that the result of GB model with -57.2477 kcal/mol is more reasonable than that of PB model with -2.53 kcal/mol.

Did I run it with something wrong? 

Many thanks

Dongman Jang

 

[Mario Ernesto]

Nothing wrong here... They would produce similar solvation energies for small molecules... not the case for bigger systems... you should also consider that in this case, PB uses a different model than GB for calculating the non-polar part of the desolvation energy (check this thread https://valdes-tresanco-ms.github.io/gmx_MMPBSA/Q%26A/calculations/#possible-solutions_2). GB as you pointed out is faster than PB.

hope this helps!

Mario E.

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[Dong Man Jang]

Oh, I understand.

When I followed the instruction as shown in the link you add, it gives different result that PB method have -40 kcal/mol, which is more reasonable for my guess. 

Nonetheless, considering the fact that the binding-free energy result from a PB method could be largely fluctuated depending what options I choose as a input parameter, it seems a bit difficult for me to use it.  

Many thanks!

Dongman Jang

2021년 7월 1일 목요일 오후 6시 28분 59초 UTC+9에 marioe911116님이 작성: