Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide

From: David A Case via AMBER <>
Date: Sun, 4 Sep 2022 09:04:25 -0400

On Sun, Sep 04, 2022, Jiaan Zhu via AMBER wrote:
>I’m trying to generate parameters of an artificial nucleotide by the following steps:
>1. Download 1WA.cif file from PDB
>2. antechamber -fi ccif -i 1WA.cif -bk 1WA -fo ac -o -c bcc -at amber
>3. prepgen -i -o 1wa.prepin -m -rn 1WA
>4.parmchk2 -i 1wa.prepin -f prepi -o frcmod.1wa -a Y -p $AMBERHOME/dat/leap/parm/parm10.dat
>There’s an error in the step 4: $AMBERHOME/bin/parmchk2: line 4: 666869 Segmentation fault (core dumped) $AMBERHOME/bin/to_be_dispatched/parmchk2 "$@“

>Does anyone know how to fix this problem? The 1WA.cif, 1wa.prepin and
> files are attached.

I don't see any attachments(?). It would be helpful to add the 1wa.prepin
file as well, since that is the actual input for the step that failed.


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Received on Sun Sep 04 2022 - 06:30:02 PDT
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