Re: [AMBER] Problem with antechamber/acdoctor

From: David Case <>
Date: Sat, 6 Oct 2018 12:54:35 +0000

On Wed, Sep 26, 2018, Sarah Fegan - UKRI STFC wrote:
> However when
> I ran antechamber a second time using the ac file as input to get a mol2
> file of the output (with the calculated charges), I got an error from
> antechamber -i -fi ac -o output.mol2 -fo mol2 -s 2 -at gaff
> Welcome to antechamber 17.3: molecular input file processor.
> acdoctor mode is on: check and diagnosis problems in the input file.

> -- Check Weird Bonds --
> /home/skfegan/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Weird atomic valence (1) for atom (ID: 1, Name: C1).
> Possible open valence.

Sorry for being to slow in replying to this email. I can't reproduce your
problem: using exactly the input given above runs for me without error.

First idea is to update to AmberTools18, if you are using an earlier version.

If that doesn't help, try turning acdoctor off (with the "-dr no" flags).
That is just a workaround, but maybe it will point to some problem. Also, let
us know what OS and compiler you are using--my tests use gcc 8.2.0 on MacOS;
it's possible that there is some compiler-version sensitive issue.


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Received on Sat Oct 06 2018 - 06:00:01 PDT
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