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 pr
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
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
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
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
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
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