AMBER TUTORIAL-1: How to simulate a protein-basic steps for md simulation in amber (AMBER 16)
BLOG #1 This blog is for beginners in MD simulation. After installation of AMBER, you may start this tutorial by choosing any protein with no ligand or water i.e. APO protein. Key points to consider: - Prepare your protein in terms of bond order, terminal capping (add ACE and NME on the N and C- terminals to prevent terminal residues interaction with the solvent), add disulfide bonds if exists in a protein structure like in the case of an immunoglobulin protein family (eg. CD28, PD-1, PD-L1, CD80, etc.), fill the missing regions or breaks in your crystal, etc. #if you have prepared the protein in Maestro (Schrodinger), change the NMA to NME, increment the residue number, convert CA to CH3 in the pdb file with help of a text editor .. see example below:) file before editing: ATOM 1011 CE1 HIS A 143 26.670 14.396 200.638 1.00 0.00 C ATOM 1012 NE2 HIS A 143 ...