[gmx-users] Regarding DSSP

[Justin Lemkul]

On 2/16/15 4:07 PM, HANNIBAL LECTER wrote:
> Thanks for your reply. Couple of things.
> I don't really know where to get older dssp binaries. I couldn't find them
> available for download in the dssp website.
>

http://swift.cmbi.ru.nl/gv/dssp/

Click on "Distributions" and at the bottom of that page, "DSSPold" is the old 
version.

> I renamed the mkdssp binary to dssp so I am sure nothing is wrong out there
> when I export the binaries for utilization in gromacs.

Aside from the usual advice of making sure the binary is actually executable 
(and actually runs, check with ./dssp -V for instance), there's little to go on 
here.

-Justin

> On Feb 16, 2015 3:45 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/16/15 3:15 PM, HANNIBAL LECTER wrote:
>>
>>> Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is
>>> not
>>> a scope to specify using the -ver command in this particular version as
>>> opposed to the newer versions (5.0.4).
>>>
>>> By '....' I meant
>>>
>>> do_dssp -f prot.xtc -s prot.tpr.
>>>
>>> How do I specify a dssp version in gromacs-4.5.6?
>>>
>>>
>> I forget when the -ver flag was introduced.  Safe bet is if you're using
>> an ancient GROMACS version, you need a similarly ancient DSSP (version
>> 1.0.x).
>>
>>   Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP
>>> 2.0.4 again. This time I am using
>>>
>>> do_dssp -f prot.xtc -s prot.tpr -ver 2
>>>
>>> The output I am getting is shown below. Not sure what is going on.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
>>> ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame       0 time
>>>
>>
>> My guess is that "mkdssp" is not actually the same thing as "dssp" - make
>> sure you've installed a real, functional dssp binary.
>>
>> -Justin
>>
>>   0.000   Back Off! I just backed up ddJszHtZ to
>>> ./#ddJszHtZ.1#----------------------------------------------
>>> ---------Program
>>> do_dssp, VERSION 5.0.4Source code file:
>>> /home/apratim/Programs/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c,
>>> line: 670Fatal error:Failed to execute command: Try specifying your dssp
>>> version with the -ver option.For more information and tips for
>>> troubleshooting, please check the GROMACSwebsite at
>>> http://www.gromacs.org/Documentation/Errors
>>> <http://www.gromacs.org/Documentation/Errors>---------
>>> ----------------------------------------------*
>>>
>>>
>> --
>> ==================================================
>>
>> 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

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