[gmx-users] Regarding DSSP

[HANNIBAL LECTER]

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.

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.
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.
>>
>>
>>
>>
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>>
>>
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>>
>>
>> *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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