Re: [AMBER] antechamber problem with negatively charged nitrogen

From: David A Case <>
Date: Fri, 18 Sep 2020 10:58:30 -0400

On Fri, Sep 18, 2020, Giorgos Lambrinidis wrote:
>I want to prepare oxypurinol molecule using antechamber module, which
>has a nitrogen charged (2 single bonds). When i run
>antechamber -i 1.sdf -fi sdf -o 11.sdf -fo sdf -c bcc -nc -1
>i get the error
>/opt/AMBER/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
>Weird atomic valence (2) for atom (ID: 3, Name: N1).
>        Possible open valence.
>the problems is found on the nitrogen which is charged (N-)

You can try setting '-dr no' to remove the valence check, and see what
happens. But be sure to check the results carefully, since you will be
outside the usual range of structures that GAFF has been built for.
You should also add '-at gaff2' to get more up-to-date parameters.

cc-ing to Junmei, in case he has comments here.


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Received on Fri Sep 18 2020 - 08:00:03 PDT
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