AMBER Archive (2004)

Subject: AMBER: VS: mmpbsa question

From: Olayiwola Adekoya (Olayiwola.Adedotun.Adekoya_at_fagmed.uit.no)
Date: Thu Apr 29 2004 - 04:32:32 CDT

 
-----Opprinnelig melding-----
Fra: Olayiwola Adekoya
Sendt: 28. april 2004 21:56
Til: amber_at_scripps.edu
Emne: mmpbsa question


Hi Amber guys,

I ran an MMPBSA calculation on a set of 500 structures from trajectories.

 

I got the following result : this is the delta column

                                   complex1 complex2

Δelec -743.63 (5.3 ) -523.56 (3.1)

Δvdw -12.87 (2.0) -19.40 (2.0)

Δint 11.59 (3.4) 40.93 (3.4)

ΔMM -744.91 ( 0.1) -502.03 (3.7)

ΔSA -4.07 (0.0) -2.54 (0.0)

ΔPB 929.22 (4.6) 593.17 (3.0)

ΔPBSA 925.15 (4.6) 590.62 (3.0)

Δ(PB +elec) 185.59 (2.8) 69.60 (2.7)

Δ(MM +PBSA) 180.24 (3.3) 88.60 (3.3)

-TS -1088.37 (3.5) -1088.37 (3.5)

I was wondering why the difference in the electrostatic contribution from MM and that from Delphi. for the complex1,the electrostatic contribution from MM is -743.63 and 929.22 from delphi while for the complex2 -523.56 and 593.17 respectively. I was wondering why they were not consistent. I used the default values in the mm_pbsa.in script for the delphi calculations.

could anyone please explain why such difference?

the other question I have is about the value for -TS, -1088.37

the inhibitor is a protein with 102 residues, what could be sources of error.

The vibrational part contribute most to it.

Thanks for your help in advance.

Layi

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu