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
--
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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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