[gmx-users] Problem in implementing do_dssp

[Justin Lemkul]

On 4/6/16 1:08 PM, Rishikesh Parulekar wrote:
> while running directly it shows do_dssp command not found.
>

You're confusing "do_dssp" (a GROMACS module) with "dssp" (which is a standalone 
binary).  do_dssp is a wrapper binary that simply calls dssp to operate on a 
frame.  What you need to prove (to us and to yourself) is that your dssp binary 
(not do_dssp) works.  If it doesn't, GROMACS has no hope of calling it to do 
anything useful.

-Justin

>
> On Wed, Apr 6, 2016 at 10:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/6/16 12:57 PM, Rishikesh Parulekar wrote:
>>
>>> Hi ErikMarklund,
>>>          Ya I have tested dssp as it shows all flags options with gmx_mpi
>>> do_dssp -h that means executable is locatable but it is not giving output
>>> after selecting group protein ends with fatal error : failed to execute
>>> command. Try specifying your dssp version with the -ver option
>>>
>>>
>> Executing gmx do_dssp is not a valid test of whether or not your dssp
>> works. That just means your gmx binary is capable of displaying help
>> information. Please do as Erik and I both suggested and try to run the dssp
>> binary directly, not via gmx do_dssp.
>>
>> -Justin
>>
>>
>> On Wed, Apr 6, 2016 at 10:14 PM, Rishikesh Parulekar <
>>> rishi05parulekar at gmail.com> wrote:
>>>
>>> Hi Justin Lemkul,
>>>> It works with gmx binary complied with mpi as u can see this is my
>>>> command
>>>> : gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 .
>>>> After executing command I am able to select group for dssp calculation
>>>> but
>>>> it ends with fatal error : failed to execute command. Try specifying your
>>>> dssp version with the -ver option
>>>>
>>>> On Wed, Apr 6, 2016 at 9:52 PM, Erik Marklund <
>>>> erik.marklund at chem.ox.ac.uk
>>>>
>>>>> wrote:
>>>>>
>>>>
>>>> Dear Rishikesh,
>>>>>
>>>>> And you have tested that your dssp runs properly on your computer? Do
>>>>> you
>>>>> run do_dssp from a script? If so, can you please show the script and
>>>>> maybe
>>>>> someone spots something?
>>>>>
>>>>> Kind regards,
>>>>> Erik
>>>>>
>>>>> On 6 Apr 2016, at 17:03, Rishikesh Parulekar <
>>>>>>
>>>>> rishi05parulekar at gmail.com> wrote:
>>>>>
>>>>>>
>>>>>> Hi all,
>>>>>> Is there any possible solution for my mentioned problem of do_dssp
>>>>>> implementation fatal error.
>>>>>>
>>>>>> regards
>>>>>>
>>>>>> On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar <
>>>>>> rishi05parulekar at gmail.com> wrote:
>>>>>>
>>>>>> my error is not regarding the mismatch of name for the software. It has
>>>>>>> recognised the software at usr/local/bin but it is showing fatal error
>>>>>>>
>>>>>> : failed
>>>>>
>>>>>> to execute command. Try specifying your dssp version with the -ver
>>>>>>>
>>>>>> option.
>>>>>
>>>>>> If the problem is with path of software the error of setenv have
>>>>>>>
>>>>>> occured.
>>>>>
>>>>>> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f
>>>>>>>
>>>>>> md.trr
>>>>>
>>>>>> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error.
>>>>>>>
>>>>>>> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar <
>>>>>>> rishi05parulekar at gmail.com> wrote:
>>>>>>>
>>>>>>> dssp executable is directly downloaded from the
>>>>>>>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use
>>>>>>>> executable file for version 2.0.4. So this is the case and it has
>>>>>>>>
>>>>>>> been kept
>>>>>
>>>>>> under path /usr/local/bin with dssp name.
>>>>>>>>
>>>>>>>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra <
>>>>>>>> sarathchandradantu at gmail.com> wrote:
>>>>>>>>
>>>>>>>> dssp executable generally gets installed as mkdssp.
>>>>>>>>>
>>>>>>>>> Check if this is the case.
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>>
>>>>>>>>> Sarath
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Sarath Chandra Dantu, PhD, ELS
>>>>>>>>> Room No. 606, New BSBE Building
>>>>>>>>> Department of Biosciences and Bioengineering
>>>>>>>>> Indian Institute of Technology Bombay
>>>>>>>>> Powai Mumbai, 400-076, India
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 6 April 2016 at 18:00, Rishikesh Parulekar <
>>>>>>>>> rishi05parulekar at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> I have named dssp executable with proper name in usr/local/bin but
>>>>>>>>>>
>>>>>>>>> still
>>>>>>>>>
>>>>>>>>>> the error persists. I have also shown the path for the dssp with
>>>>>>>>>>
>>>>>>>>> export.
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 6, 2016 at 2:27 PM, Sarath Chandra <
>>>>>>>>>> sarathchandradantu at gmail.com
>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> do_dssp is looking for /usr/local/bin/dssp and if your dssp
>>>>>>>>>>>
>>>>>>>>>> executable
>>>>>>>>>
>>>>>>>>>> has
>>>>>>>>>>
>>>>>>>>>>> some other name do_dssp will fail.
>>>>>>>>>>>
>>>>>>>>>>> Before you run do_dssp you need to set the DSSP variable.
>>>>>>>>>>>
>>>>>>>>>>> for bash environment do this:
>>>>>>>>>>>
>>>>>>>>>>> export DSSP=`which dssp-2.0.4-linux-amd64`
>>>>>>>>>>>
>>>>>>>>>>> Regards,
>>>>>>>>>>>
>>>>>>>>>>> Sarath
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Sarath Chandra Dantu, PhD, ELS
>>>>>>>>>>> Room No. 606, New BSBE Building
>>>>>>>>>>> Department of Biosciences and Bioengineering
>>>>>>>>>>> Indian Institute of Technology Bombay
>>>>>>>>>>> Powai Mumbai, 400-076, India
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 6 April 2016 at 13:16, Rishikesh Parulekar <
>>>>>>>>>>>
>>>>>>>>>> rishi05parulekar at gmail.com>
>>>>>>>>>>
>>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi dear all,
>>>>>>>>>>>>
>>>>>>>>>>>>       I am trying to analyse the secondary structure of my protein
>>>>>>>>>>>>
>>>>>>>>>>> by
>>>>>>>>>
>>>>>>>>>> using
>>>>>>>>>>>
>>>>>>>>>>>> do_dssp on gromacs-5.1.2. However it consistently showing the
>>>>>>>>>>>>
>>>>>>>>>>> fatal
>>>>>
>>>>>> error:
>>>>>>>>>>>
>>>>>>>>>>>> failed to execute command. Try specifying your dssp version with
>>>>>>>>>>>>
>>>>>>>>>>> the
>>>>>>>>>
>>>>>>>>>> -ver
>>>>>>>>>>
>>>>>>>>>>> option.
>>>>>>>>>>>> I am using dssp executable file i.e dssp-2.0.4-linux-amd64 and it
>>>>>>>>>>>>
>>>>>>>>>>> has
>>>>>>>>>
>>>>>>>>>> been
>>>>>>>>>>>
>>>>>>>>>>>> properly placed in /usr/local/bin and also command with -ver
>>>>>>>>>>>>
>>>>>>>>>>> option has
>>>>>>>>>
>>>>>>>>>> also been executed
>>>>>>>>>>>> gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg
>>>>>>>>>>>> -ver
>>>>>>>>>>>>
>>>>>>>>>>> 2
>>>>>>>>>
>>>>>>>>>> but
>>>>>>>>>>
>>>>>>>>>>> the fatal error still persists. I am actually not getting the
>>>>>>>>>>>>
>>>>>>>>>>> valid
>>>>>
>>>>>> solution after many executions.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks in advance,
>>>>>>>>>>>>
>>>>>>>>>>>> Rishikesh S. Parulekar
>>>>>>>>>>>> Research scholar,
>>>>>>>>>>>> Department of Microbiology,
>>>>>>>>>>>> Shivaji University,Kolhapur
>>>>>>>>>>>> India
>>>>>>>>>>>> --
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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

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