Dear Jason,
Sorry for incomplete information. I used MMPBSA.py and I checked the energy components. I found that the energy difference obtained from AT12 and AT13 is vibrational energy (from nmode), not GB energy. The vibrational energy were
----------------------------------------
AT12 AT13
----------------------------------------
cpx 540.8 524.6
receptor 303.3 295.5
ligand 243.9 247.9
delta -34.4 -46.9
----------------------------------------
The input is
&general
startframe=1, endframe=1,
interval=1, keep_files=0,
verbose=1,
/
&gb
igb=2, saltcon=0.0,
/
&nmode
nmode_igb=1, nmode_istrng=0.0,
drms=0.1, maxcyc=1000,
/
Any suggestion?
Thank you,
Xioling
> Date: Mon, 2 Sep 2013 12:12:23 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different
>
> On Mon, Sep 2, 2013 at 9:18 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> > Dear All,
> >
> > I have used MM/GBSA to calculate the delta G binding of DNA with Amber12
> > and AmberTools12. Next, I installed AmberTools13 and re-compiled Amber12.
> > After re-calculating the delta G binding using the same input file (igb=2,
> > other parameters were default), the obtained result (including NMODE) are
> > different
> > AmberTools12: -70 kcal/mol
> > AmberTools13: -58 kcal/mol
> >
> > Why did two versions provide different result? Which one is reasonable?
> >
>
> We don't have enough information. I'm assuming you used MMPBSA.py. In any
> case, the GB code has remained almost identical, but there have been some
> small changes to the standard SA calculation using LCPO. (You can use
> molsurf in AmberTools 13 for GB/SA, which is a better option, IMO).
>
> It would be instructive to look at exactly which terms change between
> AmberTools 13 and AmberTools 12 to properly diagnose the problem. Without
> this information I can't help isolate the problem.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Sep 03 2013 - 02:30:02 PDT
