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
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> AMBER.ambermd.org
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--
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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Received on Fri Sep 18 2015 - 18:00:04 PDT
