I believe if you shift the Na and Cl atom names one step to the left, (column
14 to 13), andinsert a space after the atom name, as in:
from:
123456789012345678901234567890123456789012345678901234567890
ATOM 1 Na Na 1 0.000 0.000 0.000 1.00 0.00 NaATOM
2 Cl Cl 2 2.820 0.000 0.000 1.00 0.00 Cl
to:
123456789012345678901234567890123456789012345678901234567890
ATOM 1 Na Na 1 0.000 0.000 0.000 1.00 0.00 NaATOM
2 Cl Cl 2 2.820 0.000 0.000 1.00 0.00 Cl
it might work, a simple sed command should do the trick, something like:
sed -i 's/ Na /Na /' *pdb
On Friday, March 24, 2023 at 10:25:42 AM GMT+1, David van der Spoel
<[email protected]> wrote:
Hi, I think I have a correct pdb file here, containing Sodium Chloride
----
TITLE MOL processed by ACT - The Alexandria Chemistry Tookit
REMARK THIS IS A SIMULATION BOX
CRYST1 28.200 28.200 28.200 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 Na Na 1 0.000 0.000 0.000 1.00
0.00 Na
ATOM 2 Cl Cl 2 2.820 0.000 0.000 1.00
0.00 Cl
ATOM 3 Na Na 3 2.820 0.000 2.820 1.00
0.00 Na
ATOM 4 Cl Cl 4 0.000 0.000 2.820 1.00
0.00 Cl
TER
ENDMDL
----
If I try to convert it to an sdf file using
obabel -ipdb MX_4.pdb -osdf -O mx4.sdf
I get:
----
MX_4.pdb
OpenBabel03242309183D
4 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8200 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8200 0.0000 2.8200 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 2.8200 C 0 0 0 0 0 0 0 0 0 0 0 0
M END
> <TITLE>
MOL processed by ACT - The Alexandria Chemistry Tookit
> <REMARK>
THIS IS A SIMULATION BOX
> <MODEL>
1
$$$$
----
Sodium is converted to Nitrogen and Chloride to Carbon. I tried meddling
with the atomtyp.txt file but to no avail. Any suggestions to make this
work as it should?
Thanks,
--
David van der Spoel, Ph.D.,
Professor of Computational Molecular Biophysics
Uppsala University.
http://virtualchemistry.org
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