[gmx-users] how to stop duplicate atoms from being deleted
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Fri Oct 23 18:48:05 CEST 2009
Thanks again for the help. I?ve given it a go but am not overly
confident or exactly sure how I would translate this method to my
system.
This is because rather than having a chain with a well defined start
and finish I have a giant covalent structure (like a web) where each
silicon is tetrahedrally bound to oxygen (as in quartz).
O?
|
?O-Si-O ?
|
O?
Here I describe my efforts so far.
I have defined a monomer (my internal unit) as an SiO4 tetrahedra.
Therefore each monomer would have to form 4 bonds with other monomers.
I have defined my internal residue like this:
; Internal residue
[ MCM_I ]
[ atoms ]
SI SI 1.280 1
O1 O1 -0.640 1
O2 O2 -0.640 1
O3 O3 -0.640 1
O4 O4 -0.640 1
[ bonds ]
SI O1
SI O2
SI O3
SI O4
O1 -SI
O2 -SI
O3 +SI
O4 +SI
As an aside-This means that each residue is not neutral as the charges
cancel out over the entire molecule and not over a single residue-I am
not sure of the implications of this.
To complicate matters, in my structure not all of the oxygens are
bonded oxygens (i.e where each O is bonded to 2 silicons, some of the
oxygens terminate in hydroxyl groups). This means that I have will
have 3 types of terminal/starting chain
1. Si, O, O, OH
2. SI, O, OH, OH
3. SI, OH, OH, OH (the group which really does terminate)
Here are my terminal and starting residues:
; terminal residue 1 (3OH groups)
[ MCM_T1 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
OH2 OH2 -0.502 1
H2 H2 0.206 1
OH3 OH3 -0.502 1
H3 H3 0.206 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI OH2
SI OH3
SI O4
OH1 H1
OH2 H2
OH3 H3
O4 -SI
; terminal residue 2 (2 OH groups)
[ MCM_T2 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
OH2 OH2 -0.502 1
H2 H2 0.206 1
O3 O3 -0.640 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI OH2
SI O3
SI O4
OH1 H1
OH2 H2
O3 -SI
O4 -SI
; terminal residue 3 (1 OH group)
[ MCM_T3 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
O2 O2 -0.640 1
O3 O3 -0.640 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI O2
SI O3
SI O4
OH1 H1
O2 -SI
O3 -SI
O4 -SI
As each of these groups could equally be starting groups-I have
defined them as such by changing the minus sign to a plus
; starting residue 1
[ MCM_S1 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
OH2 OH2 -0.502 1
H2 H2 0.206 1
OH3 OH3 -0.502 1
H3 H3 0.206 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI OH2
SI OH3
SI O4
O4 +SI
; starting residue 2
[ MCM_T2 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
OH2 OH2 -0.502 1
H2 H2 0.206 1
O3 O3 -0.640 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI OH2
SI O3
SI O4
O3 +SI
O4 +SI
; starting residue 3
[ MCM_T3 ]
[ atoms ]
SI SI 1.280 1
OH1 OH1 -0.502 1
H1 H1 0.206 1
O2 O2 -0.640 1
O3 O3 -0.640 1
O4 O4 -0.640 1
[ bonds ]
SI OH1
SI O2
SI O3
SI O4
O2 +SI
O3 +SI
O4 +SI
There are a few problems with this:
1. I don?t know how to go about splitting my large .pdb file into
monomers. At the moment it is ordered by atomtype VMD doesn?t
recognise my self- defined SiO2 tetrahedra as monomers so I can?t sort
using that. There is no way I can do this manually by looking at the
coordinates.
2. Looking at the terminal residue 1 for example, I have defined the
only non-bonded oxygen as O4-however it could equally be O1, O2 or
O3-this leads to a number of possible combinations of my terminal and
internal residues.
3. There is in fact no such thing as a terminal residue (except in the
case of Terminal residue 1 which is rare). It is more common to have a
2 OH groups on a silicon meaning the other oxygens bond to further
residues.
I can see how this method works nicely for a chain but having a four
coordinate system really complicates things! I have run a very simple
pdb file using pdb2gmx, the new .rtp file above and a handwritten .pdb
file with 2 monomers.
The result is that pdb2gmx is creating extra bonds between the
Silicon of one monomer and the oxygen of the next meaning I am getting
a 5-coordinate Silicon.
Pdb2gmx doesn?t seem to be able to distinguish based on bond distances
which oxygens belong to which monomer. The only way I can see past
this is a more elaborate naming system which would introduce yet more
combinations.
So I?m throwing this out as a last resort before I give up. Has anyone
had any success using this method for a similar system? Quartz?
Sorry for my rambling
Jenny
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> 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 it apart.
>
>> 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 protein either!
>
> For more information, see here:
>
> http://www.gromacs.org/Documentation/How-tos/Polymers
>
>> 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.
>
> -Justin
>
>> Thanks
>>
>> Jenny
>>
>>
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>> 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
>>>>
>>>>
>>>>
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>>
>>>>
>>>> _______________________________________________
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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/
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>
>>
>>
>> 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
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