Thanks Jason for your suggestions :-)
On Tue, Jun 24, 2014 at 12:31 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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.
>
> HTH,
> Jason
>
> 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
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 23 2014 - 23:30:02 PDT
