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 <david.vandersp...@icm.uu.se> 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 När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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