My feeling was implied in what I wrote before: the answer is to MD.
I have no idea how the parameter scores are arrived at. Fitting to
databases might be irrelevant for the whole. The little I understand is
that the mode one arrives at parm7/rst should matter. First, is the
structure under examination a real minimum? If not, everything is illusion
only, no matter what the parameter scores tell us.
francesco
On Sat, Sep 19, 2015 at 2:52 AM, Robert Molt <rwmolt07.gmail.com> wrote:
> Can some sort of reference be given to judge penalty scores in
> parameterization? I could not find any in the Amber manual previously
> when I once tried to examine this.
>
> On 9/18/15 1:47 PM, Jason Swails 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Robert Molt Jr.
> r.molt.chemical.physics.gmail.com
> Visiting Associate Professor of Chemistry
> Department of Chemistry & Chemical Biology
> Indiana University-Purdue University Indianapolis
> LD 326
> 402 N. Blackford St.
> Indianapolis, IN 46202
>
>
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>
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Received on Sat Sep 19 2015 - 00:30:02 PDT
