[gmx-developers] Re: Caps of the Peptide

[Walter Ash]

Abhishek Jha wrote:
> Dear List,
>  I am trying to switch to use gmx and the first problem I ran into was
> capping my peptide. I can see NME (or NAC) in the aminoacids.dat file
and
> as well as in ff*.rtp but the pdb2gmx fails to recognize it. Any
> suggestion and help will be appreciated.
> 
> Regards,
> Abhishek


Do you see something like this in the pdb2gmx output? 
-------------------------------
...
...

Checking for duplicate atoms....
N-terminus: NH3+
C-terminus: COO-
Fatal error: Atom CA not found in residue NAC24 while adding hydrogens

If you're using opls-aa, this is due to an atom naming inconsistency
between ffoplsaa.rtp and ffoplsaa.hdb.  The former calls the carbon atom
CH3 and the latter calls it CA.  Change one and it works fine.