[gmx-users] Getting a crystal topology file from pdb2gmx

Ben Tam btam125 at hotmail.co.uk
Wed Nov 11 16:21:32 CET 2015

Dear Gromacs users and Developer,

I am trying to run a simulation for a metal organic frameworks (MOFs), it is a crystallise periodic structure. The original file is in .cif format, however using material studio I converted it to .pdb file. Now I am stuck on converting .pdb file to a topology file in gromacs using 'gmx pdb2gmx'. There is an error when I  try:
Residue 'MOL' not found in residue topology database
The structure I am simulating contained Zr  atoms, henceforth there are no residues can match that. I know it is a cif file and kind of forcing it into a .pdb file. My question is this, are there better way to convert a crystal structure (.cif file) in gromacs so I can get the topology? 
Kind regards,


More information about the gromacs.org_gmx-users mailing list