[gmx-users] MD simulations of Tyrosinase using GROMACS

Dear GMX users, I am trying to carry out MD simulations with tyrosinase protein. Tyrosinase is a tyoe-3 copper protein. In its oxygen binding active site, the protein has two copper atoms that bind to two oxygen atoms in a peroxo configuration. Each copper is co-ordinated by three histidine

[gmx-users] Error while simulating Protein in SDS/Water

Dear GMX users, I am trying to simulate a protein in SDS/Water box. 1. No problems with pdb2gmx - .gro file and .top files were generated. /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/ selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 2. Created a Cubic box