[gmx-users] Problem executing do_dssp in gromacs

Aarti rana ranaaarti.hp at gmail.com
Fri Feb 27 04:25:04 CET 2015


I tried the same on a single frame also. It's been 24 hrs and still showing
running :

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
>>>
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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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