Re: [AMBER] ambpdb- Segmentation fault (core dumped)

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Wed, 28 Jun 2017 12:46:58 +0000

Hi,

I guess the command is

ambpdb -p xyz.top < xyz.crd > xyz.pdb


                   Best Regards

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Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy


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________________________________
From: Jag Silwal <jagsilwal.gmail.com>
Sent: 28 June 2017 17:46:12
To: AMBER Mailing List
Subject: [AMBER] ambpdb- Segmentation fault (core dumped)

Dear all,

I always use h++ program to process my PDB before simulation and I use
ambpdb to convert top and crd file from h++ to create new PDB for
simulation. I never had any problem until now. The protein complex I am
trying to process has four chains with total of 473 amino acid. I processed
through h++ without any problem. But when I use ambpdb -p top -c crd >
final.pdb, I get segmentation fault, core dumped message.

Any idea on how to proceed on this? Also, if you could suggest few other
sites/program that helps me to process PDB (like protonation state, flip
and all that) I would be very grateful.

Thank you

Jag
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Received on Wed Jun 28 2017 - 06:00:07 PDT