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
> > _______________________________________________
> > 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
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Received on Fri May 06 2011 - 01:30:05 PDT
