[gmx-users] do_dssp
Miguel Ángel Mompeán García
mig.mompean at gmail.com
Fri Mar 1 18:24:04 CET 2013
Hi Erik,
Since I read in the mailing list that nobody had asked about 2.1.0, just
decided to try an older version before going into the trouble itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot for your comments
2013/3/1 Erik Marklund <erikm at xray.bmc.uu.se>
> Interesting. Perhaps there are new issues with 2.1.0. Did you try to
> execute the command yourself?
>
> Erik
>
>
> On Mar 1, 2013, at 5:16 PM, 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?
>>
>>
>>
>>
>>
>> 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://vt.edu/Pages/Personal/justin>
>>>>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>> >
>>>>>>
>>>>>> ==============================****==========
>>>>>>
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