From eb205b34471990dd19ccd2b8ec8dae59d2293618 Mon Sep 17 00:00:00 2001 From: Naveen Arun Date: Fri, 12 Jul 2024 15:38:22 -0700 Subject: [PATCH] Update instructions for hydrogenation at pH 7 Signed-off-by: Naveen Arun --- Command-line_tools/babel.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Command-line_tools/babel.rst b/Command-line_tools/babel.rst index b9f8252..0a9170f 100644 --- a/Command-line_tools/babel.rst +++ b/Command-line_tools/babel.rst @@ -242,7 +242,7 @@ If you want to add hydrogens (i.e. make them all explicit) when doing the conver If you want to add hydrogens appropriate for pH7.4 when doing the conversion the command would be:: - obabel mymols.sdf -O outputfile.smi -p + obabel mymols.sdf -O outputfile.smi -p 7.4 The protonation is done on an atom-by-atom basis so molecules with multiple ionizable centers will have all centers ionized.