I will appreciate if you can please clarify some of my doubts about drug-DNA complex.
I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but everything is about protein-ligand using GROMACS. I can also use GROMACS if that gives me the results.
My DNA sequences very small (12-mer) and I want to to intercalate it with a drug molecule. I generated the DNA sequence in Chimera. My questions are as follows.
Is it possible to insert my drug at specific sequence and then do the binding energy calculation using AMBER? (1) How can I insert it and make a complex? (2) If I have to create a complex in AMBER how can I do that---reference/tutorials link will be great.
The publications I read, they downloaded the PDB file with the drug molecule and extracted the crystallographic information where the drug is attached and then they extended the sequence from there using NAB tools in AMBER. Can somebody please explain how can we do that.
Thank you so much for your time.
- I want to intercalate the drug molecule at the desired sequence I want and calculate the binding energy.