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