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

Smith, Micholas D. smithmd at ornl.gov
Wed Nov 11 16:32:53 CET 2015

Quick clarifying question:

What force-field are you trying to use?


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ben Tam <btam125 at hotmail.co.uk>
Sent: Wednesday, November 11, 2015 10:10 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Getting a crystal topology file from pdb2gmx

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,


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