AMBER Archive (2009)

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

From: Daniel Roe (droe_at_nist.gov)
Date: Mon Nov 23 2009 - 11:42:49 CST

Hi,

You said that you are running this analysis on a stripped trajectory,
but in your Ptraj output it looks like the topology file you are using
with the stripped trajectory still has information about the waters in
it. You should make sure the topology file you are using corresponds to
the input coordinates (i.e. you need a 'stripped' topology file).
Alternatively, you could try loading in the original trajectory and
putting the strip commands before the hbond commands, but that is
probably less convenient.

-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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