[gmx-users] do_dssp

[Erik Marklund]

What happens if you execute the command (/usr/local/bin/dssp/ -i  
ddQ3PqtX -o ddR1HavD) in your terminal?

Erik

On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:

> I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error  
> you got:
>
> dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
> /dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
>
> -------------------------------------------------------
> Program do_dssp, VERSION 4.6
> Source code file: /usr/local/bin/gromacs-4.6/src/tools/ 
> gmx_do_dssp.c, line:
> 667
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the  
> -ver
> option.
>
> How can I fix that?
>
> Thanks
>
>
>
>
>
>
>
> 2013/1/15 James Starlight <jmsstarlight at gmail.com>
>
>> Justin, thanks both options works perfect.
>>
>>
>> James
>>
>> 2013/1/15 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>> On 1/15/13 7:13 AM, James Starlight wrote:
>>>>
>>>> Justin,
>>>>
>>>>
>>>>  I  want to obtain timescale on X as well as number of residues  
>>>> on Y
>>>> on the xmp graph . By  default that graph has not legend so it's  
>>>> hard
>>>> to analyse it .
>>>>
>>>
>>> The legends are printed in the .xvg header.  I've never had a  
>>> problem
>>> plotting its contents (though they are usually somewhat unclear when
>> plotted
>>> together) with xmgrace -nxy scount.xvg
>>>
>>>
>>>> By the way have you forced with some problems with dppc ? Simetimes
>>>> I've obtain error like
>>>>
>>>>
>>>> There are 286 residues in your selected group
>>>> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null  
>>>> 2>
>>>> /dev/null'
>>>> Reading frame       0 time    0.000
>>>> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
>>>>
>>>>
>>>> Fatal error:
>>>> Failed to execute command: Try specifying your dssp version with  
>>>> the
>>>> -ver option.
>>>>
>>>> and I dont know how to fix it.
>>>>
>>>> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
>>>>
>>>
>>> Since dssp changed its command line options, Gromacs had to adapt as
>> well.
>>> The error tells you to use the -ver option; you should do so.   
>>> Version 2
>>> should be the default, so check to make sure you're actually using  
>>> that
>>> version and not the old dssp.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> 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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