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

[Ben Tam]

Hi Micholas,
I am using CHARMM27.
Ben

> From: smithmd at ornl.gov
> To: gmx-users at gromacs.org
> Date: Wed, 11 Nov 2015 15:26:30 +0000
> Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx
> 
> Quick clarifying question:
> 
> What force-field are you trying to use?
> 
> -Micholas
> 
> ===================
> 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,
> 
> Ben
> 
> --
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.