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" <[email protected]>:
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" <[email protected]>:
Quoting Jennifer Williams <[email protected]>:
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
[email protected] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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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
========================================
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--
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Scotland, with registration number SC005336.
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