[gmx-users] pdb2gmx -merge non interactive

Wojtyczka, André a.wojtyczka at fz-juelich.de
Fri Dec 18 18:27:27 CET 2009


"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
< 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    gmx-users at gromacs.org
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-request at 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

More information about the gromacs.org_gmx-users mailing list