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 - 11:00:04 PDT
