If you to define a torsion corresponding to rotation around a bond
between CA and CB, they should be the central two atoms.
-Dan
On Tue, Apr 7, 2015 at 6:16 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> one more question regarding choosing amber mask for the CHi-1 dihedral
> angle corresponded to the side-chain rotation (in my case of the
> aromatic residue Y or W number 255). Assuming that this dihedral
> correspond to the rotation around Ca_Cb what from the bellow 2
> possibilities will be correct:
> 1) 255:CA 255:CB 255:CD 255:CG1
> or
> 2) 255:C 255:CA 255:CB 255:CD
>
> Also syntaxis of the mask should be chosen for the Histidine?
>
>
>
> James
>
> 2015-04-02 14:38 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>> ok thanks! It works fine!
>>
>> James
>>
>> 2015-03-31 18:01 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
>>> On Tue, Mar 31, 2015, James Starlight wrote:
>>>> yes
>>>> and what those options from the mdin.in file are do?
>>>> &wt
>>>> type='DISAVI' istep1=1, istep2=10, value1=0, value2=0.0,
>>>> &end
>>>>
>>>> here exactly difference between amber 12 and amber 14: because in the
>>>> latter &wt is placed within new disang.rst file in comparison to
>>>> amber-12 (which I'm using!)
>>>
>>> Sorry: I might have been confusing before. The &wt namelists go into the
>>> mdin file, where as the &rst namelist go into the DISANG file.
>>>
>>> See the examples in $AMBERHOME/test/nmr.
>>>
>>> ...dac
>>>
>>>
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>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 07 2015 - 07:30:03 PDT
