Re: [AMBER] antechamber problem with negatively charged nitrogen

From: David A Case <>
Date: Sun, 20 Sep 2020 10:39:05 -0400

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?


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Received on Sun Sep 20 2020 - 08:00:03 PDT
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