Re: [AMBER] Distance calculations with ptraj

From: Kira Armacost <>
Date: Mon, 8 Oct 2012 20:18:03 +0000

I only used the .binpos file to check to see if it would work. I originally used the .crd file generated from the trajectory including box information. My hydrogen bond calculations worked with imaging using the .crd file so I know that's not the problem.
From: Daniel Roe []
Sent: Monday, October 08, 2012 9:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Distance calculations with ptraj


I think the BinPos coordinate format has no box information right?
Because of this, anything that requires box info (e.g. imaging) will
fail. Assuming your coordinates come from an ensemble where box size
is constant (i.e. not NTP) you can tell ptraj what box info to use
with the 'box' command:

box [x <value>] [y <value>] [z <value>] [alpha <value>] [beta <value>]
[gamma <value>]

See if that helps.


On Sun, Oct 7, 2012 at 1:23 PM, Kira Armacost
<> wrote:
> 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
> [X]
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Oct 08 2012 - 13:30:04 PDT
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