AMBER Archive (2004)

Subject: Re: AMBER: VS: mmpbsa question

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Fri Apr 30 2004 - 02:47:32 CDT


Hi,

I think that from the information you provide below it is almost
impossible to answer any of your questions. While it is not surprising
that different molecular systems yield different electrostatic
contributions, your PB+elec sums are rather disfavorable. Similar, the
-TS data looks strange to me. What you might want to do is comment the
"unlink xxxout" lines in the functions in the mm_pbsa_calceneent module.
This will give you the output files of the programs called by mm_pbsa.
Check those very carefuly for error messages etc.

Best regards

Holger

-----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

╬?elec -743.63 (5.3 ) -523.56 (3.1)

╬?vdw -12.87 (2.0) -19.40 (2.0)

╬?int 11.59 (3.4) 40.93
(3.4)

╬?MM -744.91 ( 0.1) -502.03 (3.7)

╬?SA -4.07 (0.0) -2.54 (0.0)

╬?PB 929.22 (4.6) 593.17 (3.0)

╬?PBSA 925.15 (4.6) 590.62 (3.0)

╬?(PB +elec) 185.59 (2.8) 69.60 (2.7)

╬?(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

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++                             
Dr. Holger Gohlke

J.W. Goethe-Universitńt Fachbereich Biologie und Informatik Institut fŘr Mikrobiologie Marie-Curie-Str. 9 60439 Frankfurt/Main Germany

Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826 Email: gohlke_at_bioinformatik.uni-frankfurt.de URL: http://www.rz.uni-frankfurt.de/~hgohlke ++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu