I responded to your previous email. Long story short, I think you may have
forgotten to modify the nnp pointer. See my previous email for a more
thorough discussion.
All the best,
Jason
On Tue, Nov 9, 2010 at 7:03 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> i'm not sure why you say sander does not work- please explain what you did
> and what the result is. you only specified for anal.
> what are the "original" and "modified" versions?
>
> 2010/11/9 <Yokota_Akihiro.takeda.co.jp>
>
> > ----------------------------
> > Sorry to send a mail again.
> > The title in my previous mail was blank.
> > ----------------------------
> >
> > Dear AMBER Users,
> >
> > I am studying the topology file of AMBER to modify it,
> > especially for "excluded atoms" declaration. And I found
> > a mysterious things below. Do you have any suggestions or
> > comments to me?
> >
> > Let me explain you in a simple case.
> >
> > 1. An original pdb file have only 2 water molecules, separated in 4A.
> > 2. I changed the topology file, to ignore the nonbonded interactions
> > between 2 water molecules.
> > -> 3 points are modified(NEXT number in 8th line,
> > %FLAG_NUMBER_EXCLUDEDATOMS,
> > and %FLAG_EXCLUDED_ATOMS_LIST)
> > 3. I checked the interaction energies of modified one by using Anal
> module.
> > Anal said that nonbonded interaction between 2 waters is zero. This is
> > OK.
> > 4. And optimization by Sander module is performed, but the results from
> the
> > original and the modified are definitely the same. Why does my
> > "excluded atoms" declaration not work in Sander?
> > (This indicate that Anal module correctly recognizes the "excluded atoms"
> > declaration in topology file, and the sander module does not.)
> >
> > Do you have any suggestions or comments to me?
> >
> > Thanks in advance,
> > Akihiro Yokota
> >
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> >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Nov 09 2010 - 09:30:05 PST
