[gmx-users] Problem executing do_dssp in gromacs

[Aarti rana]

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.


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/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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