[gmx-users] how to stop duplicate atoms from being deleted
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 23 16:06:44 CEST 2009
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
> 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
For more information, see here:
> 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.
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> 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
>> 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
>>> 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
>>> ATOM 2 SI MCM 1 -21.090 -1.951 -10.636 1.00 0.00
>>> ATOM 1153 O MCM 1 20.602 -18.404 -20.904 1.00 0.00
>>> ATOM 1154 O MCM 1 20.602 -18.404 -1.945 1.00 0.00
>>> 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
>>> ATOM 3734 H MCM 1 -6.616 -18.600 -14.144 1.00 0.00
>>> Any advice appreciated,
>>> Thanks in advance
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul at vt.edu | (540) 231-9080
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users