Hi Jason,
On 24 September 2010 15:58, Jason Swails <jason.swails.gmail.com> wrote:
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.
I understand it. So I did this modification below (meaning, I added what I
think was missing). Note that all other entries with CX have a copy with CT,
so I followed this logic:
C -N -CT-C 1 0.00 0.0 -4. four amplitudes
and <-- ADDED
C -N -CT-C 1 0.42 0.0 -3. phases for phi
<-- ADDED
C -N -CT-C 1 0.27 0.0 -2.
<-- ADDED
C -N -CT-C 1 0.00 0.0 1.
<-- ADDED
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 -CT-C -N 1 0.00 0.0 -4. four amplitudes
and <-- ADDED
N -CT-C -N 1 0.55 180.0 -3. phases for psi
<-- ADDED
N -CT-C -N 1 1.58 180.0 -2.
<-- ADDED
N -CT-C -N 1 0.45 180.0 1.
<-- ADDED
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.
CT-CT-N -C 1 0.00 0.0 -4. four amplitudes
and
CT-CT-N -C 1 0.40 0.0 -3. phases for phi'
CT-CT-N -C 1 2.00 0.0 -2.
CT-CT-N -C 1 2.00 0.0 1.
CT-CX-N -C 1 0.00 0.0 -4. four amplitudes
and
CT-CX-N -C 1 0.40 0.0 -3. phases for phi'
CT-CX-N -C 1 2.00 0.0 -2.
CT-CX-N -C 1 2.00 0.0 1.
CT-CT-C -N 1 0.00 0.0 -4. four amplitudes
and
CT-CT-C -N 1 0.40 0.0 -3. phases for psi'
CT-CT-C -N 1 0.20 0.0 -2.
CT-CT-C -N 1 0.20 0.0 1.
CT-CX-C -N 1 0.00 0.0 -4. four amplitudes
and
CT-CX-C -N 1 0.40 0.0 -3. phases for psi'
CT-CX-C -N 1 0.20 0.0 -2.
CT-CX-C -N 1 0.20 0.0 1.
CX-CT-C -N 1 0.00 0.0 -4. four amplitudes
and
CX-CT-C -N 1 0.40 0.0 -3. phases for psi'
CX-CT-C -N 1 0.20 0.0 -2.
CX-CT-C -N 1 0.20 0.0 1.
And this seems to have fixed my problem.
How exactly are you "running with ff10"? Are you
> loading leaprc.ff10 instead of ff99SB or ff99bsc0?
Yes
> 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.
>
I have ff99ILDN installed, but not playing with it yet.
> Good luck!
> Jason
Thanks
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<<
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Received on Fri Sep 24 2010 - 09:00:04 PDT
