PNA-DNA duplex study using 3DNA

[souviksur]

Hello Everyone,

I have done MDsimulation of PNA(peptide nucleic acid)-DNA duplex using amber suite programme, so I got trajectory files and pdbs after simulation, now I am trying to analyze those pdbs  in 3DNA using find_pair command, but in everycase I found that it showed: no basepairs found, I cannot get it, Can you please suggest me in this regard.I am sending you my pdb of the duplex. Please let me know.

regards,
SOUVIK

[xiangjun]

Hi SOUVIK,

Thanks for using 3DNA, and posting your question at the forum.

Your attached sample PDB file 'nspP.pdb' helped me trace the origin of the problem. As shown in the chemical structure of residue K19 in your PNA-DNA complex, its atomic naming clearly does not following the PDB convention for A (purine). See my blog post "PDB ATOM coordinates record". Thus the residue is not taken as a nucleotide by 3DNA (try: find_pair -s nspP.pdb stdout) to begin with, no wonder "no basepairs found".

To solve your problem, it is best to start from the source, i.e., the software (AMBER) which generates the PDB file. Alternatively, you can write a purpose-specific script to change the base names of each PNA residue following PDB naming convention for DNA/RNA. Thirdly, if there are enough interest and use cases, I may consider adapt or create such a converting script to be distributed with future releases of 3DNA.

HTH,

Xiang-Jun