DL COMP BIOTECH

BLOG #3  Hi Guys,           This is a new tutorial on how to simulate a protein-ligand system: basic steps using AMBER. Before we begin, I hope you have read our previous post on AMBER TUTORIAL-1, since I will only be providing additional information with the ligand here, rather than repeating the previous instructions. #To parameterize the ligand file, we start with Antechamber and then parmchck.  These are a series of tools for creating files for organic molecules and some protein metal centers, which can then be read into LEaP. Junmei Wang created the Antechamber suite, which is intended to be used in conjunction with the general AMBER force field (GAFF) (gaff.dat). This is the package's most crucial program. It can convert a variety of files and assign atomic charges and types to them as well. Sqm (or, alternatively, mopac or divcon), atomtype, am1bcc, bondtype, espgen, respgen, and prepgen are among the programs that antechamber runs in respo...

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    ...