When trying to standardize a set of SMILES strings from the command line, I'm getting the following type of error:
WARNING: Chiral center has wrong connectivity at atom 2 in smiles: O[C@H](C\C(=C/C=C/1\CCC[C@@](C)([C@@H](CC[C@H]([C@H](C)CCCC(O)(C)C)2)\1)2)\C(=C)[C@@H](O)C1)1
The chirality is ignored.
The command I ran from the command prompt is as follows:
standardize 2008LiData.smi -c flo-standard.xml -o 2008LiData_CL.smi >> 2008LiData_CLStand2.txt 2>&1
I am using JChem version 5.1.3, Windows XP professional OS. I attach all relevant files.
I did not receive any errors when I copied this SMILES in to the Daylight depiction utility.
The only references I've found to this type of problem in this forum suggest that this was a bug in older versions of JChem.
Am I doing something wrong?
Many thanks for any assistance.