Hi guys, I've a problem using the last Open Babel 2.3.1 in an GNU/Linux ubuntu OS. When I convert an sdf file to a mol2 (or whatever other format) using the "--partialcharge gasteiger" option, I obtain molecules with wrong partial charges.
case A) obabel -isdf mols_charged.sdf -omol2 --partialcharge gasteiger -m -O mols_gasteiger.mol2 In this manner molecules with a NEUTRAL global charge, are CORRECTLY translated in mol2. Anyway those having a *positive or negative* charge give a *WRONG* mol2 file where the total charge (calculated as the sum of partial charges in column 9) is equal to 0!!! On the other hand if I use the command without "--partialcharge gasteiger", I obtain the correct partial charges! case B) obabel -isdf mols_charged.sdf -omol2 -m -O mols_standard.mol2 Please, can anybody answer the following questions: 1) The "standard" partial charges added when the "--partialcharge gasteiger" option is NOT written as in case B, which kind of charges they are? Gasteiger? 2) Why using the "--partialcharge gasteiger" option gives wrong total charge sum on charged molecules? Can you confirm this is a BUG? Many thanks in advance! -- View this message in context: http://forums.openbabel.org/Wrong-gasteiger-atomic-partial-charges-BUG-tp4096059p4096059.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
