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

[Jennifer Williams]

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!

Below I paste an extract of my pdb file?

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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