[gmx-users] problem regarding do_dssp

sangeeta sangeeta at bic.boseinst.ernet.in
Mon Feb 5 08:04:17 CET 2007

Dear All,

       I want to analyze the secondary structure of a protein after a 10ns 
simulation run. Previously I faced difficulty in running dssp program,So in 
order to  give a test run I ran the do_dssp program  for  100ps  trajectory 
only for  a protein containing 130 residues.The program continued for more 
than 4 days, yet it was not completed, Only it was giving the intermediate 
files namely ddEyzdyf,ddKDeKnT etc, except that no ouput were produced.I do 
not understand how long it will take or whether I am encountering any 
problem , in  the manual it is mentioned that the program is very slow, But 
I am not getting any idea whether the time it is taking  is normal, or I am 
facing some problem. Please help, I need your help urgently.Thanks in 

Junior Research Fellow

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