[gmx-users] acetyl

[Mark Abraham]

Bernhard Knapp wrote:
> Hi there,
> 
> I wanted to ask if gromacs is able to deal correctly with peptides which 
> have been acetylized at the N-terminal end? if so what would be the 
> approbriate way (tool) to model the acetyl?

Various force fields have the acetyl group available as an N-terminal 
"capping" group. As such, you still follow the same general procedure 
with pdb2gmx to generate the topology, but the .rtp file needs (say) an 
"ACE" entry and in the structure file the acetyl atoms need to have a 
residue name that matches the .rtp file entry.

Mark