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--
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