[gmx-users] dssp

[Justin A. Lemkul]

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

========================================