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
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Received on Tue May 03 2011 - 11:30:02 PDT
