[gmx-users] problem regarding dssp

sangeeta sangeeta at bic.boseinst.ernet.in
Wed Jan 24 10:37:42 CET 2007

dear Sir,

  Thanks a lot for your reply.I am sorry for the fact that my subject name 
does not tally with the problem I faced.I really apologize for that.
  So I do not need to include explicitely  "pbc=xyz" in my .mdp file as it 
is already being used by default.
  Regarding dssp I used the following commands
  export DSSP=/home/debjani/dssp
  setenv DSSP /home/debjani/dssp
  do_dssp -s md.tpr -f traj.xtc 
 At the end of the program only the files namely ddEZ117f ddOWnvlx etc were 
present, but no .xpm files were there.I want to get the plot of changing of 
secondary structural elements during the run.PLease help.


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