Hi, 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 Greetings, Florian -- ------------------------------------------------------------------------------- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
