Can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation?

01 January 1970 1 3K Report

I want to study PNA using molecular dynamics simulation, can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation. If any published protocol is available, please refer me to it.

Alexey Nikitin

Good question. If anyone can suggest where to get the idealized helix parameters and types of atoms for AMBER, I would like to add this capability in a helix designer.

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