[AMBER] A confused question about calculate the binding free energy from MMPBSA.py

From: bjyx20090941 <bjyx20090941.163.com>
Date: Mon, 18 Mar 2019 09:13:28 +0800 (CST)

Dear amber:
    I have a confused question about calculate the binding free energy from MMPBSA.py.

 Recently, I am learning how to calculate the binding free energy of receptor-ligand complex in solvated environment with MMPBSA module. And now I am repeating the example of ras-raf complex in amber tutorial. But I am confused by the result as follows due to the different versions of amber, such in tutorial the result is came from amber10,and my result is come from amber16.

       I found that some parameters have changed as default values, example parameters of inp and radiopt. I have compared the results in listed:

Table 1.The average binding free energy without entropy effect of 50 frames from different amber versions (kcal/mol£©

|

 

|

Amber10(yours)

|

Amber16(me)

|
|

Different parameter

|

ipb=1,

inp=1, radiopt=0

|

ipb=2,

inp=2, radiopt=1

|
|

¦¤Emm

|

-1025.4769

|

-1060.0425

|
|

¦¤EPB

|

946.4251

|

978.3053

|
|

¦¤ENpolar/Cavity

|

-7.3062

|

-51.5872

|
|

¦¤Edisper

| 

--
|
102.4891
|
|
¦¤Gbinding (no ¦¤S)
|
-86.3579
|
-30.8353
|
In your results, the binding of ras_raf complex is favored although this is not real binding free energy.
|
| | | |
| | |
While I have done a test for choosing different parameters in amber16 with 5 frames as following:
Table 2£ºThe average binding free energy with entropy effect of 5 frames from amber16 by choose different parameters (kcal/mol£©
|
 
|
Inp=0
|
Inp=1
|
Inp=2
|
|
 
|
Radiopt=0
|
Radiopt=1
|
Radiopt=0
|
Radiopt=0
|
Radiopt=1
|
|
¦¤Emm
|
-1060.0425
|
-1060.0425
|
-1060.0425
|
-1060.0425
|
-1060.0425
|
|
¦¤EPB
|
969.7617
|
978.3053
|
969.7617
|
969.7617
|
978.3053
|
|
¦¤ENpolar
|
--
|
--
|
-7.5509
|
-51.5872
|
-51.5872
|
|
¦¤Edisper
|
--
|
--
|
--
|
107.2185
|
102.4891
|
|
¦¤Sentropy
|
-42.0761
|
-42.0761
|
-42.0761
|
-42.0761
|
-42.0761
|
|
¦¤Gbinding (no ¦¤S)
|
-90.2807
|
-81.7371
|
-97.8316
|
-34.6494
|
-30.8353
|
|
¦¤Gbinding (¦¤S)
|
-48.2047
|
-39.662
|
-55.7555
|
7.4267
|
11.2409
|
   Actually, we can see that the binding eneries with entropy effect are differents  with regulating the parameters.
   The default parameter result of amber16 is 11.2409 kcal/mol withinp =2 and radiopt=1,while the binding free energy is -55.7555 kcal/mol with inp =1 and radiopt=0. Which result i can trusted and used ?
   So I am  very confused of this default parameter result with taking depersion energy into account. And what is the favor of parameter of inp =2 comparing to inp=1.
I really hope to hear from you as soon as possible!
Best Wishes
Fangjia Fu
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Received on Sun Mar 17 2019 - 18:30:02 PDT
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