[gmx-users] pdb2gmx -merge non interactive

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Dec 18 18:01:30 CET 2009

What exactly did you try? Something like this?

pdb2gmx -f a.gro << 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
< --original message--

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