Dear Prof. David,
Can you please suggest how to make a pdb structure for DNA with two
ligands. Our NMR data showed two ligand molecules binding to a quadruplex
DNA. But I am facing problem in making the pdb structure. When I add two
datasets for the same ligand, it says
Loading PDB file: ./newcomplexamber3.pdb
-- residue 25: duplicate [ C] atoms (total 14)
-- residue 25: duplicate [ H] atoms (total 12)
-- residue 25: duplicate [ O] atoms (total 3)
-- residue 26: duplicate [ C] atoms (total 14)
-- residue 26: duplicate [ H] atoms (total 12)
-- residue 26: duplicate [ O] atoms (total 3)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Added missing heavy atom: .R<UNK 25>.A<C2 6>
Added missing heavy atom: .R<UNK 25>.A<C3 7>
Added missing heavy atom: .R<UNK 25>.A<C1 5>
Added missing heavy atom: .R<UNK 25>.A<C8 12>
Added missing heavy atom: .R<UNK 25>.A<C9 13>
Added missing heavy atom: .R<UNK 25>.A<C11 15>
Added missing heavy atom: .R<UNK 25>.A<C12 16>
Added missing heavy atom: .R<UNK 25>.A<C13 17>
Added missing heavy atom: .R<UNK 25>.A<O2 3>
Added missing heavy atom: .R<UNK 25>.A<C4 8>
Added missing heavy atom: .R<UNK 25>.A<C5 9>
Added missing heavy atom: .R<UNK 25>.A<C7 11>
Added missing heavy atom: .R<UNK 25>.A<C6 10>
Added missing heavy atom: .R<UNK 25>.A<O1 2>
Added missing heavy atom: .R<UNK 25>.A<C10 14>
Added missing heavy atom: .R<UNK 26>.A<C2 6>
Added missing heavy atom: .R<UNK 26>.A<C3 7>
Added missing heavy atom: .R<UNK 26>.A<C1 5>
Added missing heavy atom: .R<UNK 26>.A<C8 12>
Added missing heavy atom: .R<UNK 26>.A<C9 13>
Added missing heavy atom: .R<UNK 26>.A<C11 15>
Added missing heavy atom: .R<UNK 26>.A<C12 16>
Added missing heavy atom: .R<UNK 26>.A<C13 17>
Added missing heavy atom: .R<UNK 26>.A<O2 3>
Added missing heavy atom: .R<UNK 26>.A<C4 8>
Added missing heavy atom: .R<UNK 26>.A<C5 9>
Added missing heavy atom: .R<UNK 26>.A<C7 11>
Added missing heavy atom: .R<UNK 26>.A<C6 10>
Added missing heavy atom: .R<UNK 26>.A<O1 2>
Added missing heavy atom: .R<UNK 26>.A<C10 14>
total atoms in file: 778
Leap added 52 missing atoms according to residue templates:
30 Heavy
22 H / lone pair
Residue 25 and 26 are the ligands. I changed the names of the ligands and
tried. Its not working.How I change the atom names?
Please suggest.
Thanks
Maya
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Received on Tue Oct 03 2023 - 04:00:02 PDT
