>
> 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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