[gmx-users] do_dssp

[Justin Lemkul]

On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote:
> 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?
>

Supply an .m2p file to xpm2ps -di to adjust the size of each matrix element. 
There is an example in the online manual.

-Justin

>
>
>
>
> 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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-- 
========================================

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

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