Dear Amber Users,
I would like to run MD simulations with NO and CO as ligands particles.
What would be the best approach to obtain parameters? I'm having problems
with
atoms connectivity and 'weird' valences when using Antechamber.
For example when I was trying to obtain parameters for CO I did
antechamber -i CO.mol2 -fi mol2 -o CO_1.mol2 -fo mol2 -c bcc
and I got such error:
-- Check Weird Bonds --
/usr/local/src/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 1, Name: O).
Please check atomic connectivity.
Could someone help me?
I'm using AmberTools18.
Thanks in advance!
Karolina Mitusińska
PhD student
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 10 2019 - 13:30:02 PST
