[gmx-users] dssp doubt

[Emine Deniz Tekin]

Hi Justin,

Thank you for your descriptive reply.

I prepared new index.file which includes mainchain, and when I used the
do_dssp with -n index.ndx, it worked.

But, if I doesn't use the index file, again, the "Protein" is selected by
the system. It is weird..
Best regards,

Deniz
On Thu, Jun 7, 2012 at 5:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/7/12 10:07 AM, Turgay Cakmak wrote:
>
>> Hi all,
>> I downloaded the original form of DSSP which is recently called
>> DSSPold. Whenever I use the following:
>>
>> *do_dssp -s  topol.tpr  -f  t raj.xtc  -o  ss.xpm *
>>
>>
>> It selects "Protein" by it-self without any control from me. I want to
>> choose
>> from the list, for example not protein but C-alpha.
>>
>
> That shouldn't happen.  You should be prompted for a selection.  Note that
> selecting only C-alpha atoms will not work.  DSSP requires all MainChain
> atoms to be considered, since the secondary structure criteria are based on
> hydrogen bonding distances.  An incorrect selection could explain the error
> you get below.
>
> -Justin
>
>  To solve this probIem, I prepared the index file which includes only
>> C-alphas of
>> my system. Then, I use the following:
>> *do_dssp  -s  topol.tpr  -f   traj.xtc  -n   C_alpha.ndx*
>>
>>  I get the below fatal error:
>> Program do_dssp, VERSION 4.5.4
>> Source code file: do_dssp.c, line: 566
>> Fatal error:
>> Failed to execute command: /home_palamut2/mguler/dssp/**dsspcmbi -na
>> ddcblxTU
>> ddq8aNVV > /dev/null 2> /dev/null
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> Are there any suggestions or corrections? Thanks in advance..
>> Turgay
>>
>>
>>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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