[AMBER] NO and CO parameters from Antechamber

From: Markowska <markowska.kar.gmail.com>
Date: Thu, 10 Jan 2019 22:17:06 +0100

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
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 MitusiƄska
PhD student
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Received on Thu Jan 10 2019 - 13:30:02 PST
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