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General discussions (Q&As) / helical Parameters of a Modified nucleic acids
« on: February 02, 2008, 12:18:57 pm »
Hi,
I am trying to calculate the helical parameters of a modified nucleic acid xDNA, which contains 4 modified bases and the normal bases.
Each modified base contains an additional bezene ring. I ahve tried the suggestion for adding the entry for additional bases in baselist.dat file. Atomic_X.pdb files for each new entry were added in the BASEPAIRS directory. Modified adenines and Guanines were identified by the program, but the modified Thymine and Cytosine were not identified.Modified ADE and GUA have same connection atom with the sugar, but the connection atom name is different for CYT and THY. I have also tried by modified ADE as A, GUA as G etc. Here also the purines were identified and pyrimidines were not.How can I make the program identify the new residues?
Thanking You for your help,
Mathew
I am trying to calculate the helical parameters of a modified nucleic acid xDNA, which contains 4 modified bases and the normal bases.
Each modified base contains an additional bezene ring. I ahve tried the suggestion for adding the entry for additional bases in baselist.dat file. Atomic_X.pdb files for each new entry were added in the BASEPAIRS directory. Modified adenines and Guanines were identified by the program, but the modified Thymine and Cytosine were not identified.Modified ADE and GUA have same connection atom with the sugar, but the connection atom name is different for CYT and THY. I have also tried by modified ADE as A, GUA as G etc. Here also the purines were identified and pyrimidines were not.How can I make the program identify the new residues?
Thanking You for your help,
Mathew