[gmx-users] dssp

[#ZHAO LINA#]

I did choose 1 protein when it asked me to choose.

Thanks for your answering, I may try on my desktop another time.

lina
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Linus Östberg [bioinf at talavis.eu]
Sent: Friday, November 05, 2010 9:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.

// Linus Östberg

On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# <ZHAO0139 at e.ntu.edu.sg> wrote:
> 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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