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

[Justin Lemkul]

On 11/11/15 11:05 AM, Ben Tam wrote:
> 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.

The reason I ask is that the prerequisite for your work is that you have 
incorporated all of that into a GROMACS force field (or built a custom one 
yourself).  pdb2gmx does not work magic.  You need to have everything already 
laid out in terms of the charges, types, and connectivity already.  A better 
choice in your case is almost certainly x2top, because pdb2gmx is generally 
intended for linear polymers with limited branching.  x2top will determine 
connectivity from distances set in an .n2t file.  I would strongly suggest this 
for any crystalline material.  The point about a custom force field remains, though.

-Justin

> 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
>>>>
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>>>    		 	   		
>>>
>>
>> --
>> ==================================================
>>
>> 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
>>
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>   		 	   		
>

-- 
==================================================

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

==================================================