From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jan 26 2015 - 10:50:35 CST
You'll need to create and apply a patch, which is like a special residue
that modifies an existing topology.
http://www.charmm.org/documentation/c34b1/struct.html#%20Patch
You can find an example in the standard CHARMM topology for proteins is you
look for the patch for disulfide bonds (called DISU).
That patch is applied in the following psfgen example:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node17.html
Jerome
On 26 January 2015 at 17:28, luca belmonte <lucabelmonte_at_gmail.com> wrote:
> Yes, in the QM calculations I have all of them, but I did not mapped them
> into the par file.
>
> What I have done is to map everything related to the methanethiol group of
> the cysteine residue of the top/par files but I did not mapped any angle
> between the sulphurs of different cysteines (the S-M2+-S angle you said).
>
> Could you please provide me any example, keyword or manual reference to do
> that?
>
>
> 2015-01-26 17:20 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>
>> What I said was very generic. Now looking at the specific arrangement, it
>> should be possible to reliably enforce a tetrahedral shape with 6 S-Mg-S
>> angle potentials. Do you have those in your model? If yes maybe there's a
>> problem with them.
>>
>> Jerome
>>
>> On 26 January 2015 at 17:02, luca belmonte <lucabelmonte_at_gmail.com>
>> wrote:
>>
>>> Hi Jerome,
>>>
>>> Thank you for the reply.
>>>
>>> At the very beginning of the story I was wondering to do as you suggest--001a11c0dd5c1c54ac050d90f108--
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