[gmx-users] how to stop duplicate atoms from being deleted

[Justin A. Lemkul]

Jennifer Williams wrote:
> 
> Hi Justin,
> 
> Thanks for the reply. I am in fact studying one huge molecule. All of my 
> atoms are bonded together in one large structure (kind of like a 
> zeolite) so I have necessarily defined them as a single residue.
> 

I would argue that you have a polymer, which can certainly be handled by 
pdb2gmx.  See below.

> There is no way I can split this molecule into smaller subunits and thus 
> define a number of residues-it wouldn't make sense to do so.
> 

If you have a lot of repetition, I would think it would be quite easy to split 
it apart.

> Yes in my .rtp file I have only defined each atom type once. To define 
> each and every atom in my one residue would mean defining 4284 atoms!
> 

If you have a repeating structure, you have a polymer, so you can just decompose 
a repeat unit into a single .rtp entry.  That's the entire purpose of pdb2gmx, 
we certainly wouldn't want to create an .rtp entry for every single possible 
protein either!

For more information, see here:

http://www.gromacs.org/Documentation/How-tos/Polymers

> I am having real trouble in creating topology files for my structure. At 
> the moment, the only way I can do this is by using a tool in DL_POLY to 
> create a field file and then manually change it to a .top file. This is 
> really fiddely and I have a number of similar structures to do this for. 
> I was hoping that I could do a similar step in Gromacs and get a .top 
> file straight away-even if it means a bit more work setting it up.
> 
> Is there any hope or is pdb2gmx simply not designed to work for this 
> sort of system?
> 

You can certainly use pdb2gmx, it is intended to be versatile so it can be used 
with any repeating structure of monomers, homogenous (like a repeating polymer) 
or heterogenous (like a protein).  See the link above.

-Justin

> Thanks
> 
> Jenny
> 
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>> Quoting Jennifer Williams <Jennifer.Williams at ed.ac.uk>:
>>
>>>
>>> Hello
>>>
>>> I am studying a mesoporous silica for which there is no topology in
>>> gromacs-to try to automate the process of generating a topology file
>>> (x2top doesn?t work), I am using pdb2gmx (or rather trying to).
>>>
>>> I have parameters for my silica structure and have added a new section
>>> for my molecule to the .rtp file, .atp file, atommass.dat,
>>> atom_nom.dbl, nb.itp and bon.itp files.
>>>
>>> The problem is that when I use my .pdb file to generate a topology,
>>> pdb2gmx checks for duplicates and removes almost all of my atoms. It
>>> leaves only one of each type. I should have a few hundred of each atom
>>> type?here is the output from pdb2gmx?
>>>
>>> Analyzing pdb file
>>> There are 1 chains and 0 blocks of water and 1 residues with 4284 atoms
>>>    chain  #res #atoms
>>>    1 ' '     1   4284
>>> All occupancies are one
>>>
>>> All ok up to here?and then?.
>>>
>>> Processing chain 1 (4284 atoms, 1 residues)
>>> There are 552 donors and 2580 acceptors
>>> There are 1603 hydrogen bonds
>>> Checking for duplicate atoms....
>>> Now there are 4 atoms. Deleted 4280 duplicates.
>>>
>>> Can anyone explain why this is happening? ?none of my atoms have the
>>> same coordinates. Is there a file that I have forgotten to alter?  Is
>>> there is fix to turn off the checking of duplicate atoms? I don?t want
>>> any of my atoms to be deleted!
>>
>> You have all of your atoms defined within one residue.  I'm assuming 
>>  your .rtp
>> entry contains the definition of a single repeat unit, so each monomer 
>> should
>> be a separate residue.  The coordinates don't matter, it's because  
>> within each
>> residue, you have the same atom names, so pdb2gmx removes them when it 
>> finds
>> them.
>>
>>>
>>> Below I paste an extract of my pdb file?
>>>
>>
>> I'm assuming you'll have to probably reconstruct this file to 
>> re-organize the
>> atoms to define continuous residues.  It appears they are grouped by 
>>  atom name,
>> which is probably not what you want.
>>
>> -Justin
>>
>>> CRYST1   46.421   43.630   75.838  90.00  90.00 120.00 P 1           1
>>> ATOM      1  SI   MCM   1     -21.090  -1.951 -29.596  1.00  0.00   
>>>         SI
>>> ATOM      2  SI   MCM   1     -21.090  -1.951 -10.636  1.00  0.00   
>>>         SI
>>> ??..
>>> ATOM   1153  O    MCM   1      20.602 -18.404 -20.904  1.00  0.00   
>>>          O
>>> ATOM   1154  O    MCM   1      20.602 -18.404  -1.945  1.00  0.00   
>>>          O
>>> ?
>>> ATOM   3181  OH   MCM   1      -6.620 -18.769 -32.169  1.00  0.00
>>> ATOM   3182  OH   MCM   1      -6.620 -18.769 -13.210  1.00  0.00
>>> .....
>>> ATOM   3733  H    MCM   1      -6.674 -18.381 -33.035  1.00  0.00   
>>>          H
>>> ATOM   3734  H    MCM   1      -6.616 -18.600 -14.144  1.00  0.00   
>>>          H
>>>
>>> Any advice appreciated,
>>>
>>> Thanks in advance
>>>
>>>
>>>
>>> -- 
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>>
>>>
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>>
>>
>>
>> ========================================
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>>
>> ========================================
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> 
> 
> 
> Dr. Jennifer Williams
> Institute for Materials and Processes
> School of Engineering
> University of Edinburgh
> Sanderson Building
> The King's Buildings
> Mayfield Road
> Edinburgh, EH9 3JL, United Kingdom
> Phone: ++44 (0)131 650 4 861
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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