Hi Xiang-Jun
In reply to your answer to my initial question,
viewtopic.php?f=11&t=195&start=15, I have tried the steps that you suggested. I have added the .exe to line #425 of 'x3dna_md.rb'. I then executed:
x3dna_md.rb -b bpfile.dat -e sample_md0.pdb
and I think this now works. Thanks
With regards to using 'fiber', I have managed to make an ssDNA molecule but cannot work out how to form an ssRNA as it won't accept any 'Us' in my sequence. I have tried:
fiber -a, -20 rna.pdb
however this just returns the help file so I assume I've entered it wrong.
Also, Is it possible to give ssRNA molecules any secondary structures such as stem loops?
Thanks
Henry