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

From: Arun Kumar Somavarapu <>
Date: Wed, 15 Jan 2014 21:43:50 +0530


Hello David,

I have seen a similar message as you mentioned, but i didnt see any
error message other than segmentation fault.

In your earlier message you suggested me to break the molecule, as i am
new to Amber may be i will generate files for individual piece but i
have no idea about next steps (like how to link and proceed).

Is there any tutorial in which this is explained? or can you give me a
brief idea about it.

Thanking you.

On 2014-01-14 01:46, David A Case wrote:

> On Tue, Jan 14, 2014, Arun Kumar Somavarapu wrote:
>> There is no other message before core dump.
> I'm a little confused. In your earlier email, you said the that the sqm.out
> file indicated a successful completion. But now you seem(?) to say that you
> did not see the "Total number of electrons: 58; net charge: 0
> Running: /home/case/amber12/bin/sqm -O -i -o sqm.out" messages?
> Or, did you get this message but just not report it?
>> if i use glycam ff , can i use complex (protein + ligand) for input file preparation step with tleap ?
> Yes...if you have a polymer that is "similar to 8-10 glucose units", using
> Glycam is strongly recommended.
> ...dac
> _______________________________________________
> AMBER mailing list
> [1]

Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
AMBER mailing list
Received on Wed Jan 15 2014 - 08:30:09 PST
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