[gmx-users] Problem executing do_dssp in gromacs

Tue Mar 3 07:20:21 CET 2015

Thank you everyone specially Justin. Finally my do_dssp is working. Problem
was with the binary file 'dssp-2.0.4-linux-amd64
<ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>' .
Now I have installed 'dssp-2.0.4-linux-i386
<ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386>' and it is
working fine.

Cheers!!

On Sat, Feb 28, 2015 at 4:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/26/15 10:25 PM, Aarti rana wrote:
>
>> I tried the same on a single frame also. It's been 24 hrs and still
>> showing
>> running :
>>
>>
> A single frame should be done in about a second.  If it's hanging for any
> longer than that, something is wrong.  Either the binary fails (try running
> DSSP directly, not via do_dssp) or something else weird is happening, but
> there's really nothing to go on at present.
>
> -Justin
>
>
>  Select a group: 1
>> Selected 1: 'Protein'
>> There are 668 residues in your selected group
>> dssp cmd='/usr/local/bin/dssp204 -i ddNf0AkV -o ddtcC3SI > /dev/null 2>
>> /dev/null'
>> Reading frame       0 time 10000.000
>> Back Off! I just backed up ddNf0AkV to ./#ddNf0AkV.1#
>>
>>
>> On Thu, Feb 26, 2015 at 9:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 2/25/15 11:10 PM, Aarti rana wrote:
>>>
>>>  As suggested I followed the other threads too. I am writing down my
>>>> exact
>>>> steps :
>>>>
>>>> Downloaded the executable from the dssp site (dssp-2.0.4-amd64)
>>>> copied to my vaccine folder
>>>> renamed the file to dssp204
>>>>
>>>>  chmod u=rwx dssp204
>>>>> sudo mv dssp204/usr/local/bin/
>>>>> export DSSP=/usr/local/bin/dssp204
>>>>> do_dssp -f next.xtc -s next.tpr -sc scount.xvg -o ss.xpm -ver 2
>>>>>
>>>>>
>>>> The program started running. But it's been 7 days and it's still
>>>> running.
>>>> It seems there is some problem with the run.
>>>>
>>>>
>>>>  So make a small test case.  Run do_dssp on a single structure, then
>>> run it
>>> on a shorter trajectory, and see if it works.  Maybe the process is hung
>>> up, and maybe the reason is external to the program itself.  Unless your
>>> trajectory is TB in size, there's no way it should run for 7 days.
>>>
>>> -Justin
>>>
>>>
>>>
>>>  On Tue, Feb 17, 2015 at 6:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 2/16/15 9:49 PM, Aarti rana wrote:
>>>>>
>>>>>   After issuing command as you asked:
>>>>>
>>>>>>
>>>>>>    echo $DSSP
>>>>>>
>>>>>>  /usr/local/bin/dssp
>>>>>>>
>>>>>>>
>>>>>>>  And yes I downloaded the "dssp-2.0.4-linux-amd64
>>>>>> <ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64>" file
>>>>>> from
>>>>>> dssp site.
>>>>>>
>>>>>>
>>>>>>   Please see the other thread with this exact same issue as we have
>>>>>> gone
>>>>>>
>>>>> through a number of troubleshooting steps.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>>
>>>>>   On Mon, Feb 16, 2015 at 11:52 PM, Justin Lemkul <jalemkul at vt.edu>
>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>  After looking at this a bit more closely for someone else who asked
>>>>>>> the
>>>>>>> same question, your clue is here:
>>>>>>>
>>>>>>> dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2>
>>>>>>> /dev/null'
>>>>>>>
>>>>>>> For some reason your do_dssp command is triggering version 1
>>>>>>> syntax.  A
>>>>>>> version 2 command should be something like:
>>>>>>>
>>>>>>> dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2>
>>>>>>> /dev/null'
>>>>>>>
>>>>>>> Note the difference in -i/-o vs. -na.  This is the nature of the
>>>>>>> problem
>>>>>>> when dealing with different versions.  Somehow there's a disconnect
>>>>>>> between
>>>>>>> your DSSP version or the command you're telling us you're issuing.
>>>>>>>
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>
>>>>>>> Department of Pharmaceutical Sciences
>>>>>>> School of Pharmacy
>>>>>>> Health Sciences Facility II, Room 629
>>>>>>> University of Maryland, Baltimore
>>>>>>> 20 Penn St.
>>>>>>> Baltimore, MD 21201
>>>>>>>
>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
>>>>>>> Gromacs Users mailing list
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>   --
>>>>>>
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/
>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
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>>>
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>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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