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