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

From: Arun Kumar Somavarapu <>
Date: Tue, 14 Jan 2014 00:28:30 +0530


Hello Sir,

There is no other message before core dump.

when i tried leaving out -c bcc option, i got mol2 file with out

if i use glycam ff , can i use complex (protein + ligand) for input file
preparation step with tleap ?

On 2014-01-13 18:40, David A Case wrote:

> 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
> field.
> Following is only relevant if you don't wish to or cannot take the above
> advice.
>> 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"
> message?
> Try leaving out the "-c bcc" part and see what happens.
> ...dac
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> AMBER mailing list
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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 Mon Jan 13 2014 - 11:30:02 PST
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