AMBER Archive (2009)

Subject: Re: [AMBER] hbond analysis by ptraj- segmentation fault

From: Daniel Roe (droe_at_nist.gov)
Date: Mon Nov 23 2009 - 11:49:23 CST

Also, I just noticed this in your output:
"Estimated memory usage for this hbond call: 53.41 GB"
Unless you have that much memory available ptraj will choke. Try
dividing this call into subsets if possible.

-Dan

Jayalakshmi Sridhar wrote:
> Dear Amber Users,
> I am trying to do Hbond analysis using ptraj on the md trajectory file. I
> have stripped the trajectory of water and ions. I have tried running the
> script on the .mdcrd file, but everytime I get the error- Segmentation fault
> (core dumped). I am attaching the output file and also the input file. Thank
> you for the help in sorting out this problem.
> Jaya.
> 

-- 
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741

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