Hello Modeller Caretaker
I request your help with modelling nucleic acids using Modeller.
Reading through the archives, I have done the following: (1) modified the restyp.lib file for Modeller to recognise my 1-letter codes for the nucleic acids (ADE, THY, GUA, CYT), with the modified contents of the file as below: 112 | ADE | ! | ADE | 114 | CYT | + | CYT | 120 | GUA | ^ | GUA | 136 | THY | & | THY |
(2) modified my pdb file to include the 3-letter pdb codes (ADE, CYT, GUA, THY) instead of 1-letter pdb codes (A,C,G,T,) in columns 18-20 of the residue name, and
(3) have used the alignment of the modified nucleic acid codes (as specified in restyp.lib) in my alignment file.
However, I still get a bunch of warnings and a couple of errors; and I am unable to understand what changes I need to make to model nucleic acids using Modeller.
This is the final error although I cannot find any correction to make to my alignment file: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: FIRST: @.
I would appreciate your suggestions as to what I am doing incorrectly.
With thanks and regards Nisha