Hello Modeller Users

Charlotte, thank you for your reply. However, I have included the number of nucleic acid residues in the description line of the structure and sequence.

Actually, I have tried to model both the case of only nucleic acids, as well as the case of protein+nucleic acids.

(1) Modelling only nucleic acids - results in the following error: 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: @

(2) Modelling protein+nucleic acid - results in the following error: csrrng__299E> Atom index is out of bounds: 7621 7620 nselat__596E> Atom index is out of range (iatm,natm): 7621 7620

I have a question: Will Modeller allow for modelling only nucleic acids (without protein), or does it need to have the nucleic acids modelled along with protein?

I am still unable to model nucleic acids (either by itself or with protein) using Modeller and would appreciate any suggestions on corrections/changes to make.

With thanks and regards Nisha

> Hello! > > Hopefully others will have more detailed responses, but here is > something that might help you. > > In modelling my protein of interest with a ligand I obtained the same error message as you have. What I had to do was to modifiy the sequence headers in the alignment file. In the first description line for each sequence and template, the total number of residues needs to include the ligand residues. > > I am also trying to model a nucleic acid and have succeeded with a simpler (ATP) ligand just within the last few days. > > I will be working on including a tRNA in my model in the next few days/weeks and will share any useful info and tips. > > -Charlotte Habegger-Polomat > > > > > nisha@ncbs.res.in wrote: > >>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 >>_______________________________________________ >>modeller_usage mailing list >>modeller_usage@salilab.org >>http://salilab.org/mailman/listinfo/modeller_usage >