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Sir, i am trying to do dssp but it not happen what can i do.
please take a below cmd
user@user:~/Documents/Yogesh/Aromatase/24/dssp$ which dssp
/usr/bin/dssp
user@user:~/Documents/Yogesh/Aromatase/24/dssp$ Export DSSP /usr/bin/dssp
Export: command not found
user@user:~/Documents/Yogesh/Aromatase/24/dssp$ dssp -h
dssp [options] input-file [output-file]:
–dict arg Dictionary file containing restraints for residues in
this specific target, can be specified multiple times.
–output-format arg Output format, can be either ‘dssp’ for classic DSSP or
‘mmcif’ for annotated mmCIF. The default is chosen
based on the extension of the output file, if any.
–min-pp-stretch arg Minimal number of residues having PSI/PHI in range for
a PP helix, default is 3
–write-other If set, write the type OTHER for loops, default is to
leave this out
-h [ --help ] Display help message
–version Print version
-v [ --verbose ] verbose output
user@user:~/Documents/Yogesh/Aromatase/24/dssp$ gmx do_dssp -f md_0_10_center.xtc -s md_0_10.tpr -map ss.map -sc scount.xvg -o ss.xpm -tu ns
:-) GROMACS - gmx do_dssp, 2022.2 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/user/Documents/Yogesh/Aromatase/24/dssp
Command line:
gmx do_dssp -f md_0_10_center.xtc -s md_0_10.tpr -map ss.map -sc scount.xvg -o ss.xpm -tu ns
Reading file md_0_10.tpr, VERSION 2022.2 (single precision)
Reading file md_0_10.tpr, VERSION 2022.2 (single precision)
Not all residues were recognized (452 from 25244), the result may be inaccurate!
Group 0 ( System) has 81818 elements
Group 1 ( Protein) has 7399 elements
Group 2 ( Protein-H) has 3659 elements
Group 3 ( C-alpha) has 452 elements
Group 4 ( Backbone) has 1356 elements
Group 5 ( MainChain) has 1809 elements
Group 6 ( MainChain+Cb) has 2234 elements
Group 7 ( MainChain+H) has 2244 elements
Group 8 ( SideChain) has 5155 elements
Group 9 ( SideChain-H) has 1850 elements
Group 10 ( Prot-Masses) has 7399 elements
Group 11 ( non-Protein) has 74419 elements
Group 12 ( Other) has 56 elements
Group 13 ( 41) has 56 elements
Group 14 ( CL) has 5 elements
Group 15 ( Water) has 74358 elements
Group 16 ( SOL) has 74358 elements
Group 17 ( non-Water) has 7460 elements
Group 18 ( Ion) has 5 elements
Group 19 ( 41) has 56 elements
Group 20 ( CL) has 5 elements
Group 21 ( Water_and_ions) has 74363 elements
Select a group: 5
Selected 5: ‘MainChain’
There are 452 residues in your selected group
dssp cmd=‘/usr/local/bin/dssp -i ddlxqhoq 2>/dev/null’
Reading frame 0 time 0.000
Back Off! I just backed up ddlxqhoq to ./#ddlxqhoq.1#