Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped)

From: David A Case <>
Date: Tue, 14 May 2019 08:55:43 -0400

On Mon, May 13, 2019, Sadaf Rani wrote:

>Warning: Atom type (C.2) is not in PARMCHK.DAT; using default values
> for improper_flag [0], group_id [0], and equivalent_flag [0].

This is only a warning, but it could be causing the later segfault.
Try not using sybyl atom types (things like C.2), and see if that helps.
(That is, don't use the "-at sybyl" option in your antechamber runs.

Basically, parmchk is not set up to run with sybyl atom types, but error
checking is rather minimal in these programs.

...good luck....dac

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Received on Tue May 14 2019 - 06:00:02 PDT
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