Hmm... "although it is necessary to run it through on the command line once to see what the order of arguments should be"
...exactly is the main problem as I don't know all the time how many chains are in the files I'm processing. Pdb2gmx asks for every chain included in your files. Though I can assume 8 chains in 99% of the files, I wanted to know if there may be a switch included in pdb2gmx like -ff. Maybe I prescan my files to get the amount of chains and then pass that value to my pdb2gmx script. Anyway, thanks for your answer, I appreciate it! < What exactly did you try? Something like this? < < pdb2gmx -f a.gro << EOF < 5 < y < EOF < < I have not done -merge myself, but I often pass in multiple < 'command-line' arguments in a scripts, although it is necessary to run < it through on the command line once to see what the order of arguments < should be. I could be the one whose wrong as I have never done -merge, < but then again I have never had a problem automating any of the < gromacs tools and I don't see why this one should be any different. < < < -- original message -- << Hi, thanks for your answer! << << I think this only refers to the -ff force field selection. << I tried several scripting solutions to pass "y" to the pdb2gmx questions << whether to do the merging or not. << << Maybe my wires are just crossed but i did not find any hint to << get rid of this questions. << << < Can't you just do one of these: << < << < echo "5" | pdb2gmx -f a.gro << < << < or << < << < pdb2gmx -f a.gro << EOF << < 5 << < EOF << < << < --original message-- -- gmx-users mailing list [email protected] http://lists.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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- gmx-users mailing list [email protected] http://lists.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
