On Fri, May 4, 2007 at 3:25 AM, Toshifumi Yui <tyui.cc.miyazaki-u.ac.jp>wrote:
> Dear Jason M. Swails
>
> Thank for you mail.
>
> I could not find SCEE_SCALE_FACTOR entry in my topology file.
> So, it appears that I should have used Amber Tools to build it, using sleap
> only was not enough.
>
Using sleap is the only way to do it right now. Check the spelling error I
pointed out in the last email.
The fact that SCEE_SCALE_FACTOR is not there just means that you didn't do
it right.
>
> I will .check the manual and try it.
>
> Toshi Yui
>
> > On Thu, May 3, 2007 at 2:18 PM, Toshifumi Yui
> > <tyui.cc.miyazaki-u.ac.jp>wrote:
> >
> >> Dear
> >>
> >> My system is the complex of protein and carbohydrate molecules, which
> are
> >> not covalently connected.
> >>
> >> I wish to implement a job with different SCEE and SCNB values in pmemd
> of
> >> amber11, if possible (Unit value for carbohydrate and the default ones
> >> for
> >> protein.)
> >> .
> >> Here is my sleap input file.
> >>
> >> >sleap -s -f
> >> >set default write14scle on
> >>
> >
> > scale, not scle
> >
> >
> >> >source leaprc.ff99SB
> >> >source leaprc.GLYCAM_06
> >>
> >> >model = loadPdb comp.pdb
> >> >saveamberParm model comp.parm7 comp.inp
> >> >quit
> >> ~
> >>
> >> Unfortunately, it seems not to work appropriately, and probably the
> >> default
> >> scaling factors have been only assigned to all of the parameters.
> >>
> >
> > I don't know what you mean by this. It's successful if you see
> > "SCEE_SCALE_FACTOR" in your topology file (and "SCNB_SCALE_FACTOR").
> Note
> > you have to have AmberTools 1.4 or greater for this feature (and amber11
> > or
> > greater to take advantage of it).
> >
> > HTH,
> > Jason
> >
> >
> >> I wonder if I am wrong in this regards.
> >>
> >> Thank you.
> >>
> >> Toshi Yui
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 03 2011 - 23:00:02 PDT
