do_dssp no longer complies with dssp input
Since last year the dssp program has different in-/output and e.g. no longer recognizes -na, which is used by do_dssp. Preferrably do_dssp should test what kind of input dssp takes before invoking dssp. Here's the new help text from dssp:
-h [ --help ] Display help message
-i [ --input ] arg Input file
-o [ --output ] arg Output file, use 'stdout' to output to screen
-v [ --verbose ] Verbose output
-d [ --debug ] arg Debug level (for even more verbose output)
To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:
dssp.exe -i 1crn.pdb -o 1crn.dssp
#1 Updated by Erik Marklund about 8 years ago
This was apparently discussed on the user list with a quick fix (below). Still, automatic detection or manual selection of dssp version would be nice.
#2 Updated by Erik Marklund about 8 years ago
Here's a suggestion that means minimal effort for programmers. If a sevond environment variable, DSSP2, is set to the full name of the new dssp executable, then the new syntax is used. Alternatively, a command-line option could turn on the new syntax. The thing is that the old dssp is not downloadable from the dssp website, so in one way or another gromacs should learn to handle the new version.