dssp_interface
Calculate the protein secondary structure in trajectories by using DSSP
Because this is the interface program, the users should install the DSSP program in advance. The path to the binary program is specified in [OPTION]. In this program, each snapshot in the trajectory is written into temporary_pdb, and DSSP is executed for this PDB file one by one, and all results are output into outfile.
[INPUT] psffile = ../BPTI_ionize.psf # protein structure file reffile = ../BPTI_ionize.pdb # PDB file [OUTPUT] outfile = output.out # output file [TRAJECTORY] trjfile1 = ../BPTI_run.dcd # trajectory file md_step1 = 500000 # number of MD steps mdout_period1 = 500 # MD output period ana_period1 = 500 # analysis period repeat1 = 1 trj_format = DCD # (PDB/DCD) trj_type = COOR+BOX # (COOR/COOR+BOX) trj_natom = 0 # (0:uses reference PDB atom count) [SELECTION] group1 = segid:BPTI # select protein [OPTION] check_only = NO # (YES/NO) analysis_atom = 1 # protein atom group dssp_exec = /home/user/bin/dssp # dssp binary path temporary_pdb = temporary.pdb # temporary pdb file name for DSSP rename_res1 = HSE HIS rename_res2 = HSD HIS
To analyze the secondary structure properties such as the helicity, the user should write a script to analyze the output file. The following is an example of csh script to calculate the helicity, where the file name and number of residues are specified as in red color:
#!/bin/csh
set filename = output.out
set numres = `grep "TOTAL NUMBER OF RESIDUES" ${filename} | head -1 | awk '{print $1}'`
set nstr = `grep SNAPSHOT ${filename} | wc -l`
echo " total number of snapshots : ${nstr}"
echo " secondary structure formation propensity of each residue"
set i = 1
while ( ${i} <= ${numres})
set istr = `awk '{if ($4 == "H") printf("%6s \n",$1)}' ${filename} | grep " ${i} " | wc -l`
set ss = `echo "scale=5; ${istr} / ${nstr}" | bc -l | sed -e 's@^\.@0\.@g'`
echo " ${i} ${ss}"
@ i += 1
end