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!
Below I paste an extract of my pdb file?
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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