[gmx-users] Problem in implementing do_dssp

Justin Lemkul jalemkul at vt.edu
Wed Apr 6 18:22:15 CEST 2016



On 4/6/16 12:03 PM, Rishikesh Parulekar wrote:
> Hi all,
>   Is there any possible solution for my mentioned problem of do_dssp
> implementation fatal error.
>

Does the dssp binary function on its own as a standalone program (i.e. when not 
called from do_dssp)?  Does it work with a gmx binary not compiled with MPI?

-Justin

> 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
>>>>>>> --
>>>>>>> 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

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


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