Ahmed samier Mohamed

3 Questions 7 Answers 0 Followers

Questions related from Ahmed samier Mohamed

MM-GBSA per residue energy decomposition positive value?

I ran a molecular dynamics simulation for a system that consists of a peptide-protein complex, the binding happens at certain residues. on calculating the MM-GBSA per residue energy decomposition...

08 March 2022 8,096 4 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

01 February 2021 6,433 1 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

24 January 2021 4,137 7 View