[gmx-users] how to stop duplicate atoms from being deleted
Jennifer.Williams at ed.ac.uk
Fri Oct 23 14:37:15 CEST 2009
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?
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 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
>> 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
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> 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 posting!
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Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
The King's Buildings
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.
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