prasun kumar wrote: > I am trying to model a protein DNA complex.but nucleotides are not > defined in the rtp file of modeller.
Sure they are - there are topologies and parameters defined for ADE, CYT, GUA, THY (one letter codes a, c, g, t). These are RNA bases though so you'll have to apply the DEO1 or DEO2 patches to make them into DNA. And you'll have to apply 3' and 5' patches (e.g. 5TER, 5MET, 5PHO, 3TER, 3PHO) since Modeller does not do this automatically (unlike for amino acid C and N termini).
Modeller is not, however, a package for DNA modeling. If you have DNA in your template, it can reproduce it in the target, but you can't put in an unknown DNA or RNA sequence and have Modeller generate a reasonable model. If all you want to do is copy DNA from your template to the target, it's probably easier to use BLK residues and copy it rigidly.
Ben Webb, Modeller Caretaker