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

[Ben Tam]

Hi Justin,

I am using Gaussian with basis set 6-31G* and LanL2DZ to calculate the charges of the structure and using UFF for the lennard jones. When I answered CHARMM27, I am assuming the question was what is the option that was given when I typed 'gmx pdb2gmx'. In all honesty, I have no particular reason for using CHARMM or AMBER. All I want out of it is the atom to atom bonding instead of painstakingly  insert it by manual.  
Ben 

> To: gmx-users at gromacs.org
> From: jalemkul at vt.edu
> Date: Wed, 11 Nov 2015 10:50:29 -0500
> Subject: Re: [gmx-users] Getting a crystal topology file from pdb2gmx
> 
> 
> 
> On 11/11/15 10:37 AM, Ben Tam wrote:
> > Hi Micholas,
> > I am using CHARMM27.
> 
> And, out of curiosity, what is the source of your Zr parameters?
> 
> -Justin
> 
> > 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.
> >   		 	   		
> >
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> -- 
> 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.