I would like to make MD simulation of a 42-bp B-DNA double helix, which has a segment of single strand at each end of the chain, and a small molecule anti-cancer drug. I have searched PDB and NDB for the crystal information. But I do not kown how to chose a set of right data. I am a real green-hand in MD simulation. What are the key factors should I take into consideration? The ions in my buffer? The sequence of the DNA molecule?
First, the atomic-resolution model of the drug in complex with DNA. Second, the DNA sequence (can be edited if needed).
I would like to add "availability of electron density" other than what Martin has mentioned.
If you have electron density present for the structure, the structural analysis with the electron density using coot would help you to locate the modelling error in the structure if any. Which you can minimize my running re-refinement.
I would like to inform select base on expression in which and also view X-ray and NMR techniques as well as presence of Ligand not ion.
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