[gmx-users] create dihedrals' index giving the names of atoms from file

[Claus Valka]

Dear gromacs users,

my system comprises 16 polymer chains with 455 atoms
each. I want to calculate the dihedral distribution
for a number of dihedrals.

I want to create an index file which will contain the
global numbers (the third column of the gro
file-concecutive number of atoms) of the
atom-quadraplets, which will correspond to the
dihedrals I want to calculate. 

If I use the make_ndx command I have to type 'a' and
then for each dihedral angle I have to type the names
of the atoms I'm interested in (for example C1 C2 C3
C4, which are four carbon atoms in my case).

If I have already created a text file which has in
every row the names of the atoms I'm interested in,
which will be the command that will give me as output
the index file I want? I suppose that I should type
only one command.

For example the command :

make_ndx -f input_file.gro -o output_file.ndx <
input_text_file.txt

doesn't work.

And will the output be in the format gromacs wants
(four atoms in a row)? I'm asking this because when I
typed one quadraplet the format of the index file
wasn't the one it should have been.

Thank you in advance,
Nikos




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