[gmx-users] do_dssp

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Oct 29 10:19:57 CET 2008

On Wednesday, 29. October 2008, Morteza Khabiri wrote:
> Dear gmx users,
> I run the program do_dssp for my system which is too small. Unfortunately,
> I run it for a long time but I am in a doubt that it is working correctly
> or not
> because it is run for one day and i don't have any idea when it will be
> finished and also after running I have a message which said "sh:
> /usr/local/bin/dssp: is a directory" Which take me in a doubt that do_dssp
>  run correctly or not.
> Please give me at least some idea about end time of program.

have you installed dssp?

do_dssp -h

do_dssp reads a trajectory file and computes the secondary structure for each
time frame calling the dssp program. If you do not have the dssp program, get
it. do_dssp assumes that the dssp executable is /usr/local/bin/dssp. If this
is not the case, then you should set an environment variable DSSP pointing to
the dssp executable, e.g.:

setenv DSSP /opt/dssp/bin/dssp


 Dr. Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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