[AMBER] Distance calculations with ptraj

From: Kira Armacost <kza0004.tigermail.auburn.edu>
Date: Sun, 7 Oct 2012 19:23:43 +0000

I'm trying to run distance calculations on ptraj and keep getting this error:

PTRAJ: Processing input from "STDIN" ...

PTRAJ: trajin closed-FMR_avg_300ns_nowat.binpos 1 1500
  Checking coordinates: closed-FMR_avg_300ns_nowat.binpos
Segmentation fault (core dumped)

Here's my input file:

trajin closed-FMR_avg_300ns_nowat.binpos 1 1500
rms first *
center :1-361
image familiar

distance 297NH1_111OD1 :297.NH1 :111.OD1 out 297NH1_111OD1.out
distance 297NH1_111OD2 :297.NH1 :111.OD2 out 297NH1_111OD2.out
distance 297NH2_111OD1 :297.NH2 :111.OD1 out 297NH2_111OD1.out
distance 297NH2_111OD2 :297.NH2 :111.OD2 out 297NH2_111OD2.out
distance 297NE_111OD1 :297.NE :111.OD1 out 297NE_111OD1.out
distance 297NE_111OD2 :297.NE :2111.OD2 out 297NE_111OD2.out

I have my parameter file and the binpos file cleared of water and ions. I have also tried playing with the number of frames (total is 60000). Also, i've done the .crd file instead of the .binpos file and continue to get this response.

Thank you,

Kira Armacost
Auburn University
Ph.D. Candidate

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Received on Sun Oct 07 2012 - 12:30:02 PDT
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