Well, antechamber had sets atom type "cd" for the carbonyl carbon in
N-CO-NH
where the first N bears a negative (albeit delocalized) charge. The reason,
by the antecahmber point of view, is probably that that piece makes part of
a carbocycle fused to nearly aromatics. This leads to those bad scores.
I have now set atom type "c" in the ".ac" file for that carbon, as if it
were an amide carbon (as it probably is). Then, parmchk2 gives
BOND
>
> ANGLE
> c -nc-cc 66.180 120.480 same as c -nc-cd, penalty score= 1.1
> c -cd-na 67.795 118.565 Calculated using c-cd-nh, penalty score=
> 3.0
>
> DIHE
>
> IMPROPER
> n -nc-c -o 10.5 180.0 2.0 Using general
> improper torsional angle X- X- c- o, penalty score= 6.0)
> c -c -n -hn 1.1 180.0 2.0 Using general
> improper torsional angle X- X- n-hn, penalty score= 6.0)
> cd-n -c -o 10.5 180.0 2.0 Using general
> improper torsional angle X- X- c- o, penalty score= 6.0)
> c -cc-cd-na 1.1 180.0 2.0 Using the
> default value
> ca-cd-na-hn 1.1 180.0 2.0 Using general
> improper torsional angle X- X-na-hn, penalty score= 6.0)
> ca-ca-ca-na 1.1 180.0 2.0 Using the
> default value
> ca-ca-ca-ha 1.1 180.0 2.0 Using general
> improper torsional angle X- X-ca-ha, penalty score= 6.0)
> c3-ca-na-cc 1.1 180.0 2.0 Using the
> default value
> cd-na-cc-nc 1.1 180.0 2.0 Using the
> default value
>
> NONBON
>
Is that a safer starting point? Or is there something misleading behind?
I.e., simply that amides are well recognized.
I should point out that I carried out a thorough QM optimization in vacuo
of the molecule (derived, without Hs, from X-ray diffr) at RHF(UHF)/6-31G*
level, including vibrational analysis without negative frequencies. I
mentioned UHF because I had to set QM so that unpaired intervenes when
needed, otherwise one gets RHF/UHF wavefunction instability. So, no "plain"
molecule.
thanks for advice
francesco
On Fri, Sep 18, 2015 at 7:47 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Sep 18, 2015 at 12:57 PM, Francesco Pietra <chiendarret.gmail.com>
> wrote:
>
> > >
> > > Did you use parmchk2 to find the parameters? This will look through
> the
> > > database
> > >
> > > and pick out parameters that best match what is in your molecule, and
> > > assign a penalty score to show you how dissimilar your molecule is from
> > the
> > > original source of the parameters.
> > >
> >
> >
> > Thanks, I used parmchk (apparently without scores) some time ago, then I
> > forgot. parmchk2 proved useful here, however what about the following
> > scores
> >
> > BOND
> > > cd-o 623.60 1.224 same as c2- o, penalty score= 4.9
> > >
> > > ANGLE
> > > nc-cd-o 74.026 127.780 Calculated using nc-ca- o, penalty
> score=
> > > 23.5
> > > n -cd-o 74.222 123.900 Calculated using o-ca-nh, penalty
> score=
> > > 25.2
> > > c -cd-na 67.795 118.565 Calculated using c-cd-nh, penalty
> score=
> > > 3.0
> > >
> > > DIHE
> > >
> > > IMPROPER
> > > n -nc-cd-o 1.1 180.0 2.0 Using the
> > > default value
> > > c -cd-n -hn 1.1 180.0 2.0 Using
> general
> > > improper torsional angle X- X- n-hn, penalty score= 6.0)
> > > cd-n -c -o 10.5 180.0 2.0 Using
> general
> > > improper torsional angle X- X- c- o, penalty score= 6.0)
> > > c -cc-cd-na 1.1 180.0 2.0 Using the
> > > default value
> > > ca-cd-na-hn 1.1 180.0 2.0 Using
> general
> > > improper torsional angle X- X-na-hn, penalty score= 6.0)
> > > ca-ca-ca-na 1.1 180.0 2.0 Using the
> > > default value
> > > ca-ca-ca-ha 1.1 180.0 2.0 Using
> general
> > > improper torsional angle X- X-ca-ha, penalty score= 6.0)
> > > c3-ca-na-cc 1.1 180.0 2.0 Using the
> > > default value
> > > cd-na-cc-nc 1.1 180.0 2.0 Using the
> > > default value
> > >
> >
> >
> >
> > Is 25.2 too much?
> >
>
> I would say 25.2 suggests that you should be particularly cautious with
> those parameters.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 14:00:03 PDT
