Hello,
On Fri, Sep 24, 2010 at 10:42 AM, Alan <alanwilter.gmail.com> wrote:
> Hello there,
>
> I've been running some antechamber tasks and I used to use ff99SB or
> ff99bsc0 in the tleap step (i.e. antechamber -> parmcheck -> tleap)
>
> However, when running with ff10, I noticed that C -N -CT-C was getting zero
> everywhere. Looking carefully at amber11/dat/leap/parm/parm10.dat I could
> see that CX is mirroring CT almost everywhere, for example:
>
CX is the new atom type for the alpha-carbon atom (it used to be CT). This
was changed I believe because the ff99SB torsion fixes for the backbone
torsion angles were inadvertently affecting the sidechain torsions as well,
when they were not supposed to. Thus, CX was changed specifically so those
ff99SB torsion modifications (the terms you highlighted below) would NOT
affect CT atom types. How exactly are you "running with ff10"? Are you
loading leaprc.ff10 instead of ff99SB or ff99bsc0? Also, have you looked at
the DE Shaw ff99SBildn parameters? My understanding is that ff10 was
supposed to build on ff99SB, fixing the side-chain torsions in much the same
way that ff99SB fixed the backbone torsions, but that it's not yet complete
(someone please correct me if I'm mistaken). You may be better off using
the ildn force field modifications for now. This link
http://ambermd.org/news.html#ildn should bring you to the page where the
relevant files and citation information can be found.
Good luck!
Jason
>
> X -CT-N3-X 9 1.40 0.0 3.
> JCC,7,(1986),230
> X -CX-N3-X 9 1.40 0.0 3.
> JCC,7,(1986),230
> (was X -CT-N3-X )
>
>
> But for
>
> C -N -CX-C 1 0.00 0.0 -4. four amplitudes
> and
> C -N -CX-C 1 0.42 0.0 -3. phases for phi
> C -N -CX-C 1 0.27 0.0 -2.
> C -N -CX-C 1 0.00 0.0 1.
> N -CX-C -N 1 0.00 0.0 -4. four amplitudes
> and
> N -CX-C -N 1 0.55 180.0 -3. phases for psi
> N -CX-C -N 1 1.58 180.0 -2.
> N -CX-C -N 1 0.45 180.0 1.
>
> I don't see entries C -N -CT-C. Sounds like something is missing, isn't it?
>
> Cheers,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> _______________________________________________
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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 Fri Sep 24 2010 - 08:00:15 PDT
