The element symbols on the right should be in positions 77-78, or 3 positions to the right. When they’re present, they take precedence over the atom name columns, because deciphering Na = sodium vs. Na = nitrogen alpha is a pain.
Also, for what it’s worth, these should definitely be HETATM not ATOM records. The main problem is that PDB is tortured by many, many programs and is thus not particularly useful for this purpose. -Geoff On Mar 24, 2023 at 6:23:10 AM, Michael Brunsteiner via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > I believe if you shift the Na and Cl atom names one step to the left, > (column 14 to 13), and > insert 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 Na > ATOM 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 Na > ATOM 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 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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