14:03:23drmeisterShiho: Can you get the Mopac reader working today?
14:03:44drmeisterIf not - can we calculate charges using whatever interface you have using carbon?
14:06:00drmeisterThere is a weird ass corner case with zeromq in the first messages that is causing a very important response from cl-jupyter to be dropped. It's driving me crazy.
14:06:33shihoMopac doesn't work yet. I tried to build but it didn't work. We can calculate charge using carbon.
15:57:08drmeisterI fixed the problem with total bond order that was screwing up Liz’s attempts. Can you pull Cando and rebuild Cando and we will try it within emacs.
15:57:37drmeisterI can’t get the fix to Liz because the jupyter interface is broken.
15:58:01drmeisterIt should be working but something is still blocking me.
19:28:02drmeisterShiho - as a sanity check can you run this... (let ((total-charge 0.0)) (chem:map-atoms 'nil (lambda (a) (incf total-charge (chem:get-charge a))) *agg-g*) total-charge)
19:28:19drmeisterThat will add up all of the atomic charges - it better sum to 0.0
19:28:55drmeisterOr Gasteiger has something to answer for... or we do.
19:29:04drmeisterI won't start pointing fingers until you send it to us.
19:33:33shihoI got the error when I created the topology file. There is a problem with atom ATOM(:OH[residue(:NIL)@0x119dfa688]bonds[2]) the sum of bond orders is: 4 and it should never be more than 3
19:33:37drmeisterThey are not being passed explicitly, they are being set within the socket.
19:33:55drmeistershiho: That was the problem I fixed a few days ago.