Hi everyone, (sorry for posting twice, I found typos in the original post)
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-XXX ALA . . XXX . .
bond_ALA-C_=_XXX-N1
# --- DESCRIPTION OF LINKS ---
#
data_link_ALA-XXX
#
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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