Thanks, I got it solved...
Yu
-----Ursprüngliche Nachricht-----
Von: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Gesendet: Monday, January 20, 2014 6:01 PM
An: AMBER Mailing List
Betreff: Re: [AMBER] output of radius of gyration
Hi,
If you are running ptraj interactively you need to type 'go' or Ctrl-D
(EOF) to actually run what you have set up.
-Dan
On Monday, January 20, 2014, Zhuang, Yu <yu.zhuang.tum.de> wrote:
> 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 [mailto:jason.swails.gmail.com <javascript:;>]
> Gesendet: Monday, January 20, 2014 1:31 PM
> An: amber.ambermd.org <javascript:;>
> 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?)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 21 2014 - 00:00:02 PST
