[gmx-users] how to stop duplicate atoms from being deleted
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 23 14:03:18 CEST 2009
Quoting Jennifer Williams <Jennifer.Williams at ed.ac.uk>:
> 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
> 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.
> 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
jalemkul at vt.edu | (540) 231-9080
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