Re: [gmx-users] pdb2gmx -merge non interactive
Hallo André, Check the wiki: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive Oliver On Fri, Dec 18, 2009 at 10:59, Wojtyczka, André wrote: > Hi List, > > is it possible to have the -merge option in pdb2gmx set to non-interactive? > > I need to merge 8 copies of a protein into one definition (.top) because if > i don't do that all the chains are included into the .top-file. It is then not > possible for me (in an easy way) to include my restraints into the same .top > file > because that would lead to a wrong order. > > To cut a long story short... I need -merge in a script and there i don't need > interactivity at all ;) > > Thx for your time > André -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -merge non interactive
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx -merge non interactive
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx -merge non interactive
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-- << Hi List, << << is it possible to have the -merge option in pdb2gmx set to non-interactive? << << I need to merge 8 copies of a protein into one definition (.top) because if << i don't do that all the chains are included into the .top-file. It is then not << possible for me (in an easy way) to include my restraints into the << same .top file << because that would lead to a wrong order. << << To cut a long story short... I need -merge in a script and there i don't need << interactivity at all ;) << << Thx for your time << André 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx -merge non interactive
Can't you just do one of these: echo "5" | pdb2gmx -f a.gro or pdb2gmx -f a.gro << EOF 5 EOF --original message-- Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx -merge non interactive
Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
