AMBER Archive (2008)

Subject: Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Oct 30 2008 - 07:49:44 CDT

I have gone through the paper which you mentioned where a similar event. I am
using the single trajectory approach and i re-checked my input and output files.
If i want to report the free energy of binding for my system which one should i
report?
What is meant by 'situation of subtracting large numbers in an unstable way'?
Thanks a lot.
Sincere Regards,
Moitrayee

>>
>> # COMPLEX RECEPTOR LIGAND
>> # MEAN STD MEAN STD MEAN STD
>> # ======================= ======================= =======================
>> PBELE -11842.66 34.34 -11842.78 35.19 36.91 4.01
>> GBELE -11909.85 29.47 -11850.11 29.51 45.86 3.86
>
> In some respects, these are not "huge differences", but rather an indication
> of how sensitive these electostatic calculations can be to small changes in
> the solvation algorithm. Of course, you should double-check your input and
> output files, but my guess is that you are seeing a version of the situation
> described here:
>
> %A H. Gohlke
> %A D.A. Case
> %T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
> Protein-Protein Complex Ras-Raf
> %J J. Comput. Chem.
> %V 25
> %P 238-250
> %D 2004
>
> You might try different GB variants, but you may also just be in a situation
> of subtracting large numbers in an unstable way.
>
> ...good luck...dac
> 

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu