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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> > >
> > >
> > > --
> > > Bill Miller III
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-6715
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> > > 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
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Received on Sat May 07 2011 - 10:30:02 PDT
