Hi all,
Our recent research is the MD of a non-standard nucleic acid, named Glycol Nucleic Acid (GNA). The glycol unit has just three carbon atoms which differs from DNA or RNA. Moreover, the base pairs were replaced by aromatic substitutes in our system to examine the interactions.
Here come the problems. Since the backbone and ¡°base pair¡± are both non-standard:
1. How could I build a double strand helix of GNA in xleap or some other programs?
2. How could I define the force field of the non-standard residues? Just like using Antechamber to build the force field of the ligand?
I have read the tutorials already, but your suggestions could be more helpful.
Thanks for you time!
Mu Xia,
Zhejiang University, China
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Received on Thu Dec 06 2012 - 01:30:03 PST
