Hello Brian, OpenBabel is correct to interpret your "Bromine" as a Boron. In the absence of the element symbol column, the element symbol is taken from columns 13 and 14. See section "ATOM" subsection "Detail" in the PDB format specification. http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html I don't know why the atom name is not preserved. Ling From: "Bennion, Brian" <benni...@llnl.gov> To: "openbabel-discuss@lists.sourceforge.net" <openbabel-discuss@lists.sourceforge.net> Sent: Thursday, November 19, 2015 4:17 PM Subject: [Open Babel] atom names stripped in OBminimize <!--#yiv1754873102 _filtered #yiv1754873102 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;}#yiv1754873102 #yiv1754873102 p.yiv1754873102MsoNormal, #yiv1754873102 li.yiv1754873102MsoNormal, #yiv1754873102 div.yiv1754873102MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:"Calibri", "sans-serif";}#yiv1754873102 a:link, #yiv1754873102 span.yiv1754873102MsoHyperlink {color:blue;text-decoration:underline;}#yiv1754873102 a:visited, #yiv1754873102 span.yiv1754873102MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv1754873102 span.yiv1754873102EmailStyle17 {font-family:"Calibri", "sans-serif";color:windowtext;}#yiv1754873102 .yiv1754873102MsoChpDefault {font-family:"Calibri", "sans-serif";} _filtered #yiv1754873102 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv1754873102 div.yiv1754873102WordSection1 {}-->Hello I recently noted with the help of a colleague that atom names were not being output properly after an OBminimization operation on a pdb file, especially one that contains a Bromine atom. The command I use is obminimize –ff UFF –sd –n 5000 –opdb ligand.pdb > ligandMin.pdb The input ligand looks like this. REMARK LIG ATOM 1 O1 LIG 1 5.811 -0.667 -1.538 ATOM 2 C1 LIG 1 5.526 -0.301 -0.356 ATOM 3 C2 LIG 1 6.376 -0.204 0.681 ATOM 4 N1 LIG 1 7.739 -0.535 0.487 ATOM 5 O2 LIG 1 8.391 -0.399 1.516 ATOM 6 N2 LIG 1 4.154 0.022 -0.194 ATOM 7 C3 LIG 1 3.472 0.290 1.081 ATOM 8 C4 LIG 1 1.966 0.316 0.783 ATOM 9 C5 LIG 1 1.902 0.770 -0.676 ATOM 10 N3 LIG 1 0.653 0.271 -1.375 ATOM 11 C6 LIG 1 -0.500 1.269 -1.393 ATOM 12 C7 LIG 1 -1.071 1.580 0.008 ATOM 13 Br1 LIG 1 -2.451 2.974 -0.194 After minimization I have this: REMARKLIG COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 O LIG 1 5.910 -0.355 -1.445 1.00 0.00 O HETATM 2 C LIG 1 5.473 -0.035 -0.347 1.00 0.00 C HETATM 3 C LIG 1 6.424 0.152 0.808 1.00 0.00 C HETATM 4 N LIG 1 7.798 -0.131 0.417 1.00 0.00 N HETATM 5 O LIG 1 8.544 -0.115 1.547 1.00 0.00 O HETATM 6 N LIG 1 4.130 0.144 -0.177 1.00 0.00 N HETATM 7 C LIG 1 3.523 0.507 1.080 1.00 0.00 C HETATM 8 C LIG 1 2.043 0.231 0.823 1.00 0.00 C HETATM 9 C LIG 1 1.898 0.610 -0.655 1.00 0.00 C HETATM 10 N LIG 1 0.674 0.122 -1.330 1.00 0.00 N HETATM 11 C LIG 1 -0.498 1.020 -1.251 1.00 0.00 C HETATM 12 C LIG 1 -1.106 1.221 0.159 1.00 0.00 C HETATM 13 B LIG 1 -2.254 2.326 0.069 1.00 0.00 B Am I doing something incorrect? Thanks Brian Bennion ------------------------------------------------------------------------------
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