[gmx-users] pdb2gmx -merge non interactive

[chris.neale at utoronto.ca]

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--