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