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

[Jennifer Williams]

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.

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.

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!

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?

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


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.