[Chimera-users] Building ACE, NME (peptide caps)

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 16 11:49:28 PDT 2008

On Oct 16, 2008, at 6:22 AM, Francesco Pietra wrote:

> Hi Elaine:
> Thanks.
> Is it possible with Chimera to cap the the protein termini (once the
> work below is carried out) with ACE and NMA residues? I have no
> experience with such a procedure.
> francesco

Hi Francesco,
I wouldn't recommend doing it in Chimera.  If you are using AMBER  
anyway, do it with that program.

In Chimera, you could do it by using Build Structure (under Tools...  
Structure Editing), Modify Atom section.  It would take several cycles  
of atom modification, being careful to name the residues ACE and NME  
and to give the atoms the correct types and names as you build out.   
For the first atom in the new residue you would use "change modified  
residue's name to ACE" (or NME) and then for the rest of the atoms in  
the residue, leave the residue name unchanged.
Then, because the names of hydrogens added while building aren't  
standard for those residues, either delete all the hydrogens and re- 
add them using AddH, or use Modify Atom to change the hydrogen names  
to what AMBER expects (shown below), or just write out the file and  
use a text-editor to change their names.  It is easy to make mistakes  
in this long process.

In addition, I just found a bug where addh still thinks the first  
amino acid has a free N-terminus even though it is capped by ACE, so  
if you use addh, you would then have to delete the two hydrogens on  
the first amino acid's nitrogen and then use Build Structure (Modify  
Atom) on that nitrogen to make it trigonal and get one hydrogen back,  
and then change the name of that hydrogen to H.  THEN you would get  
correct charges from addcharge.

The atom names that AMBER (and addcharge) expect:
for ACE:  C O CH3 HH31 HH32 HH33
for NME:  N H CH3 HH31 HH32 HH33

If you are capping the residues to avoid terminal charges on residues  
that are not really the termini, there is no need to do this.  AddH  
looks at the SEQRES information in the file to decide what is really a  
terminal residue.  If it is not a real terminus (for example, the  
structure starts at residue 5 because 1-4 are disordered), the residue  
will still be treated as an internal residue  starting with NH-CA- 
(etc.) not as NH3+-CA-(etc.).  The C-terminus is handled similarly,  
(...)C(=O) if not a real terminus instead of (...)CO2 minus for the  
real C-terminus.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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