Dear All
I did 10ns simulation of three peptide residue solvated in water. Each
peptide residue is 26 residue long. In final .gro file it is showing total
78 residue which is O.K. as 3x26=78. For inserting three similar peptide I
used genconf command. when I run dssp I get total residue as 80. The command
for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the
output of dssp run is as follows.
@ s0 legend "Structure"
@ s1 legend "Coil"
@ s2 legend "B-Sheet"
@ s3 legend "B-Bridge"
@ s4 legend "Bend"
@ s5 legend "Turn"
@ s6 legend "A-Helix"
@ s7 legend "5-Helix"
@ s8 legend "3-Helix"
0 46 24 0 0 7 10 36 0 3
10 39 26 0 0 15 4 35 0 0
20 37 29 0 0 11 4 33 0 3
30 37 32 0 0 11 2 35 0 0
40 36 31 0 0 10 6 30 0 3
50 41 30 0 0 9 10 31 0 0
Please suggest why I am not getting the actual number of residue in dssp
file.
When I follow the same procedure for full protein molecule simulation I get
the same number of residue in dssp output as well as final.gro file
shahid nayeem
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