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

[Justin A. Lemkul]

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
>
>
>
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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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