[gmx-users] do_dssp
Erik Marklund
erikm at xray.bmc.uu.se
Sat Mar 2 18:25:21 CET 2013
Hi,
I'll try out the 2.1.0 with do_dssp and see if there's something
problematic with this new version. Good thing you brought it up.
Erik
On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote:
> 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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