Re: [AMBER] antechamber problem with negatively charged nitrogen

From: Giorgos Lambrinidis <>
Date: Mon, 21 Sep 2020 11:07:01 +0300


Thank you for your reply. Regarding our knowledge Nitrogen 3 must have 2
single bonds in order to carry the negative charge. O1 and O2 must have
double bond with carbon 11 and carbon9 respecively.

The structure generated has single bond between Carbon9 and Oxygen1
suggesting negative charge to the oxygen1 instead of nitrogen3. If this is
correct i have to check it again. The question is why antechamber changed
the ionization from nitrogen to oxygen? I shall check the literature and i
shall come back later.


> On Fri, Sep 18, 2020, Giorgos Lambrinidis wrote:
>>I tried the flag -dr no. The resulting structure had wrong conectivities
>>and the overall charge was 0 and 1 carbon had 5 bonds.
> I can't reproduce this. I used your file as input, and did this:
> antechamber -i 1.sdf -fi sdf -o 11.mol2 -fo mol2 -c bcc -nc -1 -dr no
> I used mol2 output since I'm more familiar with that file format.
> The result is attached. The charges add up to -1; you can check your
> and sqm.out file to get more info about charges. I don't see any
> carbon atoms that have five bonds -- which carbon is it for you?
> ....dac
> _______________________________________________
> AMBER mailing list

“Good judgement is the result of experience and experience the result of
bad judgement.”
― Mark Twain
Dr George Lambrinidis
Researcher & Laboratory Assistant Staff
School of Health Sciences
Faculty of Pharmacy
National & Kapodistrian University of Athens
tel:  +30 2107274304
      +30 2107274521
fax:  +30 2107274747
AMBER mailing list
Received on Mon Sep 21 2020 - 01:30:02 PDT
Custom Search