Hi I need a little help in using Linux. I wrote this script for the bash, that I called g_select_script.sh:
#!/bin/bash g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.4 of resname ISO' -on make_ndx -f mol_in_water.pdb -o index2.ndx cat index2.ndx index.ndx > index3.ndx make_ndx -f mol_in_water.pdb -n index3.ndx -o index_final.ndx trjconv -n index_final.ndx -f mol_in_water.pdb -s mol_in_water.pdb -o output.pdb After this I make a file called parameters_for_g_select_script, that looks like: 2 q 2|7 q 8 And finally I type in the bash this command: ./g_select_script.sh < parameters_for_g_select_script Sadly this does not work. It works correct until make_ndx -f mol_in_water.pdb -n index3.ndx -o index_final.ndx with parameters 2|7 and q The numbers of the groups are correct. I guess, that 2|7 is not transfered correctly. I tried '2|7' and "2|7" that also do not work. What is wrong in my automation? Please help a Linux noob like me. Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
