HI Abhisek, I had the same problem a few years back. Here is the solution I came up with thanks to help from the CCP4bb:
1) Add pointer atom in Coot NH2 and create link to C-terminal residue (Coot: Extensions -> Modeling -> Make link) 2) create cif file with correct link description (see below) 3) modify LINK record in PDB file to correct residues/ link name (TYR-NH2 if you use the file below with modifications for your case) 4) refine in Refmac with cif as LIB in Augie Pioszak sent me the cif file copied below. you will have to change PHE to TYR for your particular case. Hope that helps. Best, Bernhard ------------------------------- Bernhard, You need a link record in the pdb file to link the NH2 amino group to your last peptide residue. When I did this a few years back I had to include a .cif library file describing the link for use with Refmac. See pdb entry 3c4m and below for the lib description I used. I still use O, so not sure how coot handles it, but I would guess it will recognize the NH2 group just fine. Hope this helps. Regards, Augie Pioszak # --- 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 PHE-NH2 PHE . . NH2 . . bond_PHE-C_=_NH2-N # ------------------------------------------------------ # # --- DESCRIPTION OF LINKS --- # data_link_PHE-NH2 # 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 PHE-NH2 1 C 2 N single 1.329 0.020 loop_ _chem_link_angle.link_id _chem_link_angle.atom_1_comp_id _chem_link_angle.atom_id_1 _chem_link_angle.atom_2_comp_id _chem_link_angle.atom_id_2 _chem_link_angle.atom_3_comp_id _chem_link_angle.atom_id_3 _chem_link_angle.value_angle _chem_link_angle.value_angle_esd PHE-NH2 1 O 1 C 2 N 122.000 1.600 PHE-NH2 1 CA 1 C 2 N 118.200 2.000 loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd PHE-NH2 plane1 1 CA 0.020 PHE-NH2 plane1 1 C 0.020 PHE-NH2 plane1 1 O 0.020 PHE-NH2 plane1 2 N 0.020 # ------------------------------------------------------ --------------------------------------------------------------------- > On Oct 12, 2017, at 2:53 PM, Abhishek Anan <[email protected]> wrote: > > Dear all, > > I am trying to solve the structure of a peptide with C-terminal amide. In > order to add the amide group to the c-terminal TYR, I substituted TYR with > TYC (tyrosinamide) and created a link between the preceding GLY and TYC. When > refined in refmac, the pdb inserts a TER card between GLY and TYC and no > covalent bond is created between them. How do I fix this? I have also tried > to add NH2 pointer atom to TYR in coot and create a link between them but in > vain. I also imported the NH2.cif file into coot and tried to make a link but > of no use. I also tried to import NH2.cif into Jligand so I could get a link > record but it refuses to open the NH2.cif file. > > I would greatly appreciate any help! > > Best regards, > Abhishek
