Hi Tobias,
  Thank you for the reply. Your solution works as advertised!

  Perhaps this should be mentioned in the documentation.

Best,
Jernej

On Tue, Jan 27, 2015 at 5:38 PM, Tobias Beer <[email protected]> wrote:
>> Some Google Fu showed the following as a solution {{block{ ...}}}
>
>
> that's TWc, indeed
>
>>   I have a numbered list that has some bullet points or sections in the
>> middle like this
>
>
> You need to wrap the stuff you want nested in html elements. You can either
> use pre directly...
>
> # N-terminus: ACE residue
> # C-terminus: NH2
> # Before using pdb2gmx edit both terminals so they look like this:
> #* N-terminal<pre>ATOM      1  CH3 ACE     0
> ATOM      2 HH31 ACE     0
> ATOM      3 HH32 ACE     0
> ATOM      4 HH33 ACE     0
> ATOM      5  C   ACE     0
> ATOM      6  O   ACE     0
> </pre>
> #* C-terminal<pre>ATOM     84  N   NH2     5
> ATOM     85  H1  NH2     5
> ATOM     86  H2  NH2     5
> TER      87      NH2      5
> END
> </pre>
> # Relax generated peptides (few hours in auto mode).
>
> or...
>
> # N-terminus: ACE residue
> # C-terminus: NH2
> # Before using pdb2gmx edit both terminals so they look like this:
> #* N-terminal<p>
>
> ```
> ATOM      1  CH3 ACE     0
> ATOM      2 HH31 ACE     0
> ATOM      3 HH32 ACE     0
> ATOM      4 HH33 ACE     0
> ATOM      5  C   ACE     0
> ATOM      6  O   ACE     0
> ```
> </p>
> #* C-terminal<p>
>
> ```
> ATOM     84  N   NH2     5
> ATOM     85  H1  NH2     5
> ATOM     86  H2  NH2     5
> TER      87      NH2      5
> END
> ```
> </p>
> # Relax generated peptides (few hours in auto mode).
>
> Whereas those newlines in the second example (before the initial backticks)
> is important, unfortunately.
>
> Best wishes, Tobias.
>
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