so the
255:C (or N ) 255:CA 255:CB 255:CD
should correspond to mask for the dihedral around which side-chain
rotate regarding backbone e.g flip-flop or switching in the aromatic
rings, shouldn't it?
I've asked because in one of the tutorial I've found usage of the
below mask instead what seemed strange for me
255:CA 255:CB 255:CD 255:CG1
James
2015-04-07 16:23 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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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>
>
>
> --
> -------------------------
> 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
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Received on Tue Apr 07 2015 - 08:00:02 PDT
