Show Posts
1
General discussions (Q&As) / using x3dna to analyze a coarse grained model mapped into an atomistic model
« on: February 23, 2016, 10:36:59 am »
Hello,
I have a coarse grained DNA model(two bead model one for bases and the other for phosphates and sugar or backbone) and using NAB (from Amber) I have mapped it into an atomistic CG model. the primary structure is about 400 base pairs. when I feed it to X3DNA it just recognize 75 base pairs and not the rest.
I also receive the following warnings after executing the code:
***Warning: structure with overlapped base-pairs***
This structure contains intra-chain direction reverse
(I have attached the pdb file of the model if you are interested to have a look).
Thanks in Forward for your help!
I have a coarse grained DNA model(two bead model one for bases and the other for phosphates and sugar or backbone) and using NAB (from Amber) I have mapped it into an atomistic CG model. the primary structure is about 400 base pairs. when I feed it to X3DNA it just recognize 75 base pairs and not the rest.
I also receive the following warnings after executing the code:
***Warning: structure with overlapped base-pairs***
This structure contains intra-chain direction reverse
(I have attached the pdb file of the model if you are interested to have a look).
Thanks in Forward for your help!