[gmx-users] do_dssp

[Miguel Ángel Mompeán García]

The issue I mentioned was with dssp-2.1.0.  I changed to 2.0.1 and it works
fine. However, when converting the xpm to eps I get I plot very small,
where one barely can see the colour code and the legend is sooo big. Does
anyone know how to change that?





2013/3/1 Erik Marklund <erikm at xray.bmc.uu.se>

> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>
>>>> ==============================**==========
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