>
> 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?
Not yet tried how the obtained parm7/rst behave under MD.
thanks
francesco
On Fri, Sep 18, 2015 at 1:36 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Sep 18, 2015 at 3:46 AM, Francesco Pietra <chiendarret.gmail.com>
> wrote:
>
> > Hello:
> > I am trying to get the FF for a "small" molecule bearing a pseudoaromatic
> > tricyclic system. Antechamber assigns atom type "cd" (= "cc") to a
> carbonyl
> > carbon comprised, in a six-atom cycle, between to N atoms
> >
> >
> > -N-CO-NH-
> >
> >
> > In consequence, a number of unknowns arises:
> >
> > BOND K(kcal.mol-1.ang-2) Dist0(ang) Source
> > cd-o
> >
> > ANGLE K(kcal.mol-1.rad-2) Theta0(deg) Source
> > c -cd-na
> > n -cd-o
> > nc-cd-o
> >
> > DIHEDRAL Path V(kcal.mol-1.rad-1) Phase(deg.) Period Source
> >
> > IMPROPER V(kcal.mol-1.rad-1) Phase(deg.) Period Source
> > ca-ca-ca-na
> > cd-na-cc-nc
> > c -cc-cd-na
> > n -nc-cd-o
> > c3-ca-na-cc
> >
> > Such data are not available in gaff.dat even on replacing "cd" with "cc".
> > I could replace "cd" with "c", but in a perhaps too blind way of doing.
> >
>
> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Sep 18 2015 - 10:00:07 PDT
