Dear Catherine
Is your SUU an amino acid modified on the side chain side? If yes
then you can use standard peptide links. For this your SUU should be
declared as L-peptide in the description. Can you send description of
your SUU and I can try to sort out what is going on.
Garib
On 26 Feb 2008, at 22:47, Catherine Regni wrote:
Hi everyone,
I'm trying to refine a structure with a modified amino acid. I'm
running into problems connecting my modified amino acid to the
protein (making a C-N bond). Refmac runs fine, but gives an error,
"link found between C - N1, not to be used." Here is what I'm
doing-- any insights to what I'm missing would be greatly appreciated.
I've added a LINK record to my pdb file, and below is the LINK
record from my dictionary generated via ccp4i gui review
restraints-- the modified residue is XXX:
# --- LIST OF LINKS ---
#
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ALA-SUU ALA . . SUU . .
bond_ALA-C_=_XXX-N1
# --- DESCRIPTION OF LINKS ---
#
data_link_ALA-SUU
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
ALA-XXX 1 C 2 N1 . 1.260 0.020
# ------------------------------------------------------
Catherine Regni, Ph.D.
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