[gmx-users] dssp

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 5 15:03:51 CET 2010 

On 6/11/2010 12:57 AM, #ZHAO LINA# wrote:
> Last email the paths really look messy, because as I said before,
>
> I modified by mine hand before posted it.
>
> Sorry about that. I did export the path before. :-)

People who might spend their time to give free help are not at all 
interested in things that have been filtered through someone's head. If 
the contents of the heads were fully correct, then there wouldn't be a 
problem. Please follow the instructions literally, and report what you 
did literally when seeking help - that means cut and paste commands and 
outputs!

Mark

> Thanks,
>
> 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 9:53 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] dssp
>
> #ZHAO LINA# wrote:
>> But right now I noticed something a bit funny,
>>
>> Try different times,
>>
>> Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1#
>>
>> -------------------------------------------------------
>> Program do_dssp, VERSION 4.0.7
>> Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471
>>
>> Fatal error:
>> Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy>  /dev/null 2>  /dev/null
>>
>>
>> Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz>  /dev/null 2>  /dev/null
>> Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax>  /dev/null 2>  /dev/null
>> Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k>  /dev/null 2>  /dev/null
>>
>> was something wrong with mine DSSP, except path reason.
>>
> I still think you're setting your DSSP environment variable wrong.  Please
> consult the link I posted before - you have to point DSSP to the *actual
> executable* not the directory that contains it, i.e.:
>
> WRONG: export DSSP=/opt/bin
>
> RIGHT: export DSSP=/opt/bin/dssp
>
> -Justin
>
>> Thanks,
>>
>> lina
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of #ZHAO LINA# [ZHAO0139 at e.ntu.edu.sg]
>> Sent: Friday, November 05, 2010 9:35 PM
>> To: Discussion list for GROMACS users
>> Subject: RE: [gmx-users] dssp
>>
>> Hi,
>>
>> 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the "real and true" path to a simple way as it showed "pathTo..." before I posted.
>>
>> 2. seems not about root things, cause every body can write and read to/from /dev/null
>>
>> 3. I will try another time ?!
>>
>> Thanks,
>>
>> 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 9:32 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] dssp
>>
>> Linus Östberg wrote:
>>> 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.
>>>
>> The original message indicates the wrong executable was called.  The reasons
>> might still be unclear at this point, but instead of executing "dssp," do_dssp
>> was executing "pathToDSSP" instead.
>>
>> The group for analysis is also debatable.  I have seen hangs and seg faults when
>> "Protein" is selected, and other times it works fine.  The only absolute
>> requirement is that (at least) all "MainChain" atoms be considered.  The latest
>> version of GROMACS seems to handle "Protein" just fine, but older versions did
>> not.  I have no explanation for that, however :)
>>
>> -Justin
>>
>>> // 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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>> --
>> ========================================
>>
>> 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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> --
> ========================================
>
> 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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> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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