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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Received on Tue Apr 07 2015 - 05:30:04 PDT
