Re: [AMBER] Antechamber Segmentation fault (core dumped)

From: David A Case <>
Date: Mon, 13 Jan 2014 08:10:25 -0500

On Mon, Jan 13, 2014, Arun Kumar Somavarapu wrote:
> I was trying to run antechamber for my molecule which is similar to a
> polymer of 8-10 glucose units.

That sounds like too large a molecule in general for antechamber, and you
should consider either breaking it into pieces, or using the Glycam force

Following is only relevant if you don't wish to or cannot take the above

> antechamber -i out_hy.pdb -fi pdb -o out_hy.mol2 -fo mol2 -c bcc
> sqm.out file shows --------- Calculation Completed ---------- at the
> end.
> after that its giving an error of Segmentation fault (core dumped) by
> dumping a file which iam attaching here.

The core dump file is of no real use to others. Is there any other message
printed out? What is printed to the terminal right before the "core dump"

Try leaving out the "-c bcc" part and see what happens.


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Received on Mon Jan 13 2014 - 05:30:04 PST
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