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 <jalem...@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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