[gmx-users] How to add "an acetyl functional group" in the PDB file

[Mark Abraham]

xuji wrote:
> Hi all gmx users:
>  
> I need to simulate a protein with its N-terminus acetylated. I've 
> already have the protein PDB file, but I don't know how to
> add the acetyl functional group informations to the PDB file. Can 
> someone give me some methods?

Various forcefields have an acetyl residue for this purpose. Look in the
.rtp file and see what you have available. You may need to rename the
residue for the atoms that should be in ACE and not the N-terminal
residue proper.

Mark