[gmx-users] dssp

[#ZHAO LINA#]

Hi, 

Thanks for your response, I modified that path parts when I posted that information.

So my environment set was correct.

I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places.

lina

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

#ZHAO LINA# wrote:
> Hi,
>
> Program do_dssp, VERSION 4.0.7
> Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471
>
> Fatal error:
> Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null
> 2> /dev/null
>
> It came out two or three file like  ddEPI6I2 and then died like above.
>
> My first time try dssp, so do not know how to examine it.
>

Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
"pathToDSSP" as the executable.

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

Note that you should substitute a meaningful PATH on your system, not something
like "pathToDSSP."

-Justin

> Thanks for any advice,
>
> lina
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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