[gmx-users] Problem executing do_dssp in gromacs

[Justin Lemkul]

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
>>
>> ==================================================
>> --
>> 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

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