Actually, in the amber minimization/heating described before, I had user
the PyRED mol2 output generated with C2 atom of "c" type (related to the
N-C2(O)-NH of the "dirty" fused cycle).
In contrast, with the charmm minimization/heating I had used the direct
antechamber output with its assignment of atom C2 to the "cd" type. This is
the only difference in atom types between the amber and the charmm runs.
So, after your sound analysis, I hoped that, by following antechamber's
desire to maintain planarity of the cycle, i.e., using the PyRED mol2
output with C2 atom of the "cd" type, everything should be in order. That
was not the case, the described deformation of the cycle, and of the C-O-P
angle, proved to be about the same as described before (minimization with
timestep 0.1, then 1.0 and heating to 300K, where I had to decrease the
timestep to 0.001 to avoid system instability.
I checked the atom types in "mol2" and antechamber original "ac": exactly
the same, in the same order. Hope to slowly understand why, as it is
clearly my problem, having all documentation on the computer.
thanks
francesco pietra
On Mon, Sep 21, 2015 at 1:23 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, Sep 21, 2015 at 6:11 AM, Francesco Pietra <chiendarret.gmail.com>
> wrote:
>
> > The outcome of MD was most disappointing, and a remedy applied most
> > intriguing.
> >
> > The largest ligand had been optimized, and no negative frequencies arose
> > (Gaussian at the computer center). The gaussian log gave the RESP partial
> > charges and mol2 on the PyRED server. Minimization (NAMD 2.10, water box,
> > neutralized), even at timestep 0.001, caused a vast deformation of one of
> > the three cycles (the one bearing N-CO-NH that I discussed before), and
> of
> > the C-O-P angle (phosphate phosphorus). Gradual heating to 300k with
> > timestep 0.001 did not correct the structure. Very good parmchk2 score
> > notwithstanding, I had to conclude that the parameterization by analogy
> > (antechamber parmchk2) was no good.
> >
>
> This sounds like a misassignment of atom types to me. A region that
> *should* be planar but gets deformed would result from assigning atoms that
> *should* be aromatic to atom types that are not; this is what I suspect may
> have happened (you should check this carefully in your generated mol2
> file).
>
> If this is what happened, then database scores can still be very good,
> since it finds good matches with the assigned atom types -- it is simply
> the assigned atom types that are wrong. You can try to fix these by hand
> in the mol2 file (and run it through parmchk2 again) and see if you get
> more reasonable behavior.
>
> For a problem this severe, I would expect atom type misassignments to be
> fairly obvious.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 21 2015 - 10:00:03 PDT
