Re: [AMBER] output of radius of gyration

From: Zhuang, Yu <>
Date: Mon, 20 Jan 2014 14:01:48 +0000

Hi, my input file is too large, therefore I can only type in the command as following
First I use ptraj to read the prmtop file:
/ptraj 2q2m_wat.prmtop.
which results in: PTRAJ
/precessing input from ''STDIN''
then I read the mdcrd file:
/trajin 2q2m_wat_md2.mdcrd
which results in:
/PTRAJ: trajin 2q2m_wat_md2.mdcrd
/Checking coordinates: 2q2m_wat_md2.mdcrd
/Rank: 0 Atoms: 24481 FrameSize: 594914 TitleSize: 81 NumBox: 3 Seekable 1
Then I ues the command of radgyr out protein.dat mass to get the radius of gyration.
Which results in:
/PTRAJ: radgyr out protein.dat mass
/Mask [*] represents 24481 atoms
However, the ourput file is without any content. And the log file shows
/DU_create_process (./utils/launch/launch.c:593): execvp error on file radgyr (No such file or directory)

Do you think it is because of my simulation or just because of the command ?
Thanks and regards, Yu
-----Ursprüngliche Nachricht-----
Von: Jason Swails []
Gesendet: Monday, January 20, 2014 1:31 PM
Betreff: Re: [AMBER] output of radius of gyration

On Mon, 2014-01-20 at 11:13 +0000, Zhuang, Yu wrote:
> Dear Amber users,
> I have one question regarding output of radius of gyration from Amber
> 12. I have finished my simulation and results in two outputs, e.g.
> file.prmtop and file.mdcrd. however when I want to use 'ptraj' and
> 'trajin' to export radius of gyration, it always results in to a file
> with empty content. I used the command like this: radgyr out
> protein.dat mass
> Do anyone meet same problem before? how can I solve it?

Does your trajectory have any frames in it? Was there a problem reading the trajectory? I suggest providing your *exact* input file
(copy-and-paste) as well as the exact output you get from ptraj (have you tried cpptraj instead?)


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 20 2014 - 06:30:02 PST
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