[gmx-users] problem regarding dssp

sangeeta sangeeta at bic.boseinst.ernet.in
Thu Jan 25 13:32:09 CET 2007

Dear Tsjerk,

      Previously I send you the intermediate files which are the output of 
DSSP,as per your request, I think I should submit the input files also, so 
here I am attaching the .mdp and .xtc files, the command I used was 
do_dssp -s md.tpr -f traj.xtc.I want to get the particular type of plot of 
secondary structural elements over time as stated in the manual.I 
downloaded  DSSP from the link

and according to the instruction unpacked by using the command  "unzip 
dsspcmbi.zip  ", the dssp program by itself ran successfully with the typed 

"dsspcmbi PDBSourcefile DSSPDestinationfile  ", and I could view the 
destination file with all the structural informations. But when I tried to 
correlate with Gromacs by using  "do_dssp -s md.tpr -f traj.xtc" the 
intermediate files are only produced.I understand that something is going 
wrong but can not detect it, please help.Thanks in advence.

Sangeeta Kundu
Junior Research Fellow
Bose Institute, Kolkata

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