marigold

Hi, All, I tried to use convert_to_atomic.py to convert the oxDNA coarse-grained configuration file to atomistic PDB file, but I got the folllowing error message: Traceback (most recent call last): File "./convert_to_atomic.py", line 15, in <module> from scipy.optimize import _numdiff ImportError: cannot import name _numdiff</module> Could anyone tell me what to do with this error message? Thanks!

I read your post about the position of the backbone. But how to calculate the position of base site and stacking site for oxDNA2 model? Thanks a lot!

Hi All, I am trying to use oxDNA2 model to run simulation for DNA origami. Since the DNA origami system is usually very large, in my case I want to freeze some specified nucleotides(i.e., vibarating around their target positons) while the rest nucleotides move freely ( Brownian Dynamics). Is there any command or option that I could use to freeze those specified nucleotides? I could not find the documentation for oxDNA2 model which states how to calculate the positions for backbone site, base site...

Hi All, In the input file , I set seed=time(NULL). After executing "oxDNA input", I got the folllowing info DEBUG: Initializing INFO: seeding the RNG with 0 .......... My problem is that seed for the random number generator is always 0. Is there anyone who could tell me why the seed is always 0? Thanks a lot.

Hi all, I have an easier way to generate the top file with specified sequence. 1)http://bionano.physics.illinois.edu/cadnano2pdb This web sever will help convert cadnano file into pdb file with specified sequence. Note that the pdb file generated here has to be adjusted a little bit based on the standard pdb file. 2)http://tacoxdna.sissa.it/PDB_oxDNA This webe server will help convert pdb file into top and conf files required by oxDNA.

I really appreciate your detailed explanation. What letter do I need to designate for those empty squares in cadnano? Is M the number of helices or the length of the helices? I just intuitively think M is the number of helices. Probably I am wrong. Just want to double check.

I did check this page before I came here. But the paragraph about "Choosing the sequence" is very confusing to me. Could you please tell me more about how to specify the sequence in caca.sqs file? Thanks.

Hi , Flavio, Thanks for your reply. May I ask how I'm supposed to list the nucleotide sequences in the caca.sqs? I mean, should I just list the sequence of scaffold chain from 3'- 5'? Or should I list the sequences for both scaffold and staple chains? Thanks again.