Hi Abhisek (and BB),
I use the attached cif file. It has an NH2 residue defined as a peptide and gets automatically linked to the peptide chain in the buster procedure I use. So if your last residue is Tyr 100, you add NH2 101 as a HETATM in the peptide chain.
I have not tested it with Refmac though.
Best,
Herman
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Bernhard Lechtenberg
Gesendet: Freitag, 13. Oktober 2017 00:13
An: [log in to unmask]
Betreff: [EXTERNAL] Re: [ccp4bb] C-terminal amide
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 <[log in to unmask]> 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
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