AMBER Archive (2004)

Subject: Re: AMBER: questions on mm_pbsa

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue May 18 2004 - 10:18:24 CDT

Dear Jianwen,

which amber version are you using? Does the ligand or receptor taken
alone (not as a complex) work with GB? How did you prepare your prmtop
file, which GB version are you using?

Best regards

Holger

"Fang, Jianwen" schrieb:
>
> Dear amber users,
>
> I am trying to use mm_pbsa.pl to calculate binding affinity of a
> protein-ligand complex. I was able to repeat the whole tutorial and
> everything seems OK. However I ran into some problems when I started to
> calculate my complex. PB worked just fine but GB apparently did not
> work well. I found the following in the log file when I ran binding
> study:
>
> =>> Reading files
> Reading sah_417_com.all.out
> Entry 0 PB PB 0 exists -> overwriting
> WARNING: Missing GB for GB in 0 -> Taken from -1
> Entry 0 PB PB 1 exists -> overwriting
> WARNING: Missing GB for GB in 1 -> Taken from 0
>
> In com.all.out file I found follows:
> 1
> BOND = 2573.8846 ANGLE = 7059.6739 DIHED =
> 8399.9910
> VDWAALS = -7332.9080 EEL = -65871.6796 EGB =
> nan
> 1-4 VDW = 3154.7355 1-4 EEL = 37661.6334 RESTRAINT =
> 0.0000
> corrected reaction field energy: 0.0000 kt
> corrected reaction field energy: -17849.06 kt
> surface area = 32697.632
>
> I also did stability study and found GB was 0 in this case.
>
> # MEAN STD
> # =======================
> ELE -27670.16 307.43
> VDW -4169.52 46.25
> INT 17981.91 84.92
> GAS -13857.77 308.59
> PBSUR 176.62 25.43
> PBCAL -10975.52 202.31
> PBSOL -10798.91 197.35
> PBELE -38645.68 128.98
> PBTOT -24656.68 142.60
> GBSUR 234.50 33.78
> GB 0.00 0.00
> GBSOL 234.50 33.78
> GBELE -27670.16 307.43
> GBTOT -13623.27 318.96
>
> Could anybody let me know what went wrong?
> Thanks in advance,
> --Jianwen
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

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

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für 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