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

From: ABEL Stephane 175950 <Stephane.ABEL.cea.fr>
Date: Mon, 13 Jan 2014 20:20:45 +0000


If you molecule is formed with large number Glucose units, you could use the RED server [1] or the RED server python [2] to derive the atomic partial charges to be used with the Glycam force field. You will also find many examples in the RED.DB [2] how to derive charges for complex molecules with glucoses.

[1] http://q4md-forcefieldtools.org/REDS/
[2] http://q4md-forcefieldtools.org/REDS-Development/
[3] http://q4md-forcefieldtools.org/REDDB/index.php

Good luck !


Stéphane Abel, PhD
CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
Bat 528 Porte 11
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
De : Arun Kumar Somavarapu [arunks.imtech.res.in]
Date d'envoi : lundi 13 janvier 2014 19:58
À : AMBER Mailing List
Objet : Re: [AMBER] Antechamber Segmentation fault (core dumped)

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [1]

Arun Kumar Somavarapu
Project Fellow,
Dr. Pawan Gupta Lab,
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
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Received on Mon Jan 13 2014 - 12:30:03 PST
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