Re: [AMBER] MM/PBSA calculation.

From: Jason Swails <>
Date: Mon, 23 Jun 2014 15:01:27 -0400

On Mon, 2014-06-23 at 22:51 +0530, Him Shweta wrote:
> Thanks Jason for your inputs, I saw the table in Amber14 manual.
> **********Input file that i am using for calculation is as
> below*************
> &general
> endframe=100, interval=1, keep_files=0, strip_mask=:WAT, Na+,
> /
> &gb
> igb=2,
> /
> &pb
> exdi=80, indi=1.0,
> inp=1, cavity_surften=0.00542, cavity_offset=0.92,
> fillratio=4, scale=2.0, prbrad=1.4, radiopt=0,
> /
> *******For entropy calculation using NMode, the input file is:-************
> &general
> endframe=100, keep_files=0, strip_mask=:WAT, Na+,
> /
> &nmode
> nmstartframe=1, nmendframe=100,
> nminterval=1, maxcyc=10000, drms=0.001,
> nmode_igb=1,
> /
> So, using the above input file i calculated the binding energy and entropy.
> I am using ff99 force filed for running simulation in NPT ensemble using
> TIP3P water model.
> When i calculated the binding energy and entropy without setting default
> radii to mbondi2 before saving the topology files for ligand, receptor and
> complex.
> The result that i got is Delta G=-21.46 kcal.mol and TdeltaS= -20.32
> kcal/mol.
> And when i calculated the binding energy and entropy after setting the
> PBRadii to mbondi2.
> The result that i got is Delta G=-22.02 kcal.mol and TdeltaS= -13.44
> kcal/mol.
> Here in both the calculation value of entropy has changed much and value of
> delta H is more or less within the error limit.
> I need your comments and suggestions on this.

It's hard to answer a question that is not asked (but alas I will try).
If your question is "why does the entropy estimate change by 7 kcal/mol
with new radii", I don't have a good answer.

I imagine the second derivatives of the effective radii are more
sensitive to the intrinsic radius set than the effective radii
themselves, which means the normal mode frequencies will probably be
affected by different radius sets more than energies will be. While
this makes conceptual sense to me, the strongest support I have for this
explanation are the results you report here. It could be with more
stringent minimization (i.e., reducing drms to 1e-6 or something) the
difference will decrease. I really don't know for sure.


P.S. -- In the future actually ask a question. The more specific you
can make your question, the easier it will be for us to answer.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 23 2014 - 12:30:02 PDT
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