Re: [AMBER] Ptraj crashes and Hbond analysis

From: Kamali Sripathi <>
Date: Wed, 23 Mar 2011 09:01:05 -0400

Dear Dr. Cheatham,

Thank you very much for your response.

On Tue, Mar 22, 2011 at 7:33 PM, Thomas Cheatham III <> wrote:

> There is insufficient information provided to comment.
This is very true; sorry for not being more specific. The ptraj script that
I'm referring to has about 18 distance commands, one angle command, and
three dihedral commands. My system is an RNA system of 85 nucleotides, and
I've been running simulations on the wild-type structure as well as 8
structures with 1 base pair mutated. I slightly modify some distance
commands in my ptraj script to apply it to each of the 9 structures. I'm
frustrated because it works for, say, mutants 2-8, but I consistently get
seg faults when I use it for the wild-type and mutant 1 structures.

Please let me know if you need more information.

Thanks again, and have a great day,

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Received on Wed Mar 23 2011 - 06:30:02 PDT
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