When you say the delta INT value is not zero, what is it? How far away from
zero is it? Did you have any errors or warning messages when you created
your topology files? Did you use the same radii set for all the prmtops? Can
you post complex, receptor, ligand, and delta energy values? Did
mm_pbsa.plprovide you with any warning or error messaged either?
Another suggestion might be to try using MMPBSA.py released with the new
AmberTools 1.5. This MM-PBSA script has a lot of error/warning catching
messages, particularly in regards to topology inconsistencies that might be
of use here.
I hope that helps.
-Bill
On Sat, May 7, 2011 at 1:15 PM, mirage . <m.o.m.live.fr> wrote:
>
> Any Help please
>
> > From: m.o.m.live.fr
> > To: amber.ambermd.org
> > Date: Fri, 6 May 2011 08:24:11 +0000
> > Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
> >
> >
> > 1) Did you use the single or triple trajectory approach to calculate
> binding energy?
> > -> Single trajectory
> >
> > 2) I assume you are talking about the delta INT value, not the
> individual INT values
> > -> Yes
> >
> > 3) It is usually easiest to make all the necessary prmtop files at the
> same time to
> > help prevent these types of errors.
> > ->I regenerated *.prmtop from *.prep and do mm_pbsa calculation but i
> found the same INT!!!
> >
> > 4) This may not be the issue, but without more information this problem
> is difficult to diagnose
> > -> What informations?
> >
> > > Date: Thu, 5 May 2011 15:31:04 -0400
> > > From: dwight.mcgee.gmail.com
> > > To: amber.ambermd.org
> > > Subject: Re: [AMBER] internal energy INT is not zero in mm_pbsa
> > >
> > > Hi,
> > >
> > > Just to add to what Bill has already stated in the previous email. Did
> you
> > > use the single or triple trajectory approach to calculate binding
> energy?
> > >
> > > On Thu, May 5, 2011 at 3:26 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
> > >
> > > > I assume you are talking about the delta INT value, not the
> individual INT
> > > > values. This is often due to inconsistencies in the prmtop files. It
> is
> > > > usually easiest to make all the necessary prmtop files at the same
> time to
> > > > help prevent these types of errors.
> > > >
> > > > This may not be the issue, but without more information this problem
> is
> > > > difficult to diagnose.
> > > >
> > > > -Bill
> > > >
> > > > On Thu, May 5, 2011 at 3:15 PM, mirage . <m.o.m.live.fr> wrote:
> > > >
> > > > >
> > > > > Hi
> > > > > The internal energy term INT is not zero, in a single trajectory
> mm_pbsa
> > > > > calculations.
> > > > >
> > > > >
> > > > > What's wrong??
> > > > > Thanks in advance for any help
> > > > >
> > > > >
> > > > > _______________________________________________
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> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Bill Miller III
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-6715
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > T. Dwight McGee Jr.
> > > Quantum Theory Project
> > > University of Florida
> > > Graduate Student
> > > dwight.mcgee.gmail.com
> > >
> > > "Problems cannot be solved at the same level of awareness that created
> > > them."
> > > Albert Einstein
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sat May 07 2011 - 10:30:03 PDT
