[gmx-users] dssp doubt
Emine Deniz Tekin
edeniztekin at gmail.com
Thu Jun 7 16:44:00 CEST 2012
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..
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
>> 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.
> 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
>> ddq8aNVV > /dev/null 2> /dev/null
>> For more information and tips for troubleshooting, please check the
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> Are there any suggestions or corrections? Thanks in advance..
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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