[gmx-users] Problem executing do_dssp in gromacs

[Justin Lemkul]

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
>>>>>>
>>>>>> ==================================================
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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
>>>>
>>>> ==================================================
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>>>> 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/
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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

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