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

[Mark Abraham]

Claus Valka wrote:
> 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.

You're on the right track, see 
http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive

> For example the command :
> 
> make_ndx -f input_file.gro -o output_file.ndx <
> input_text_file.txt
> 
> doesn't work.

Your file needs to have the same content as you'd type interactively... 
so that means the "a" as well. Otherwise, since you haven't really told 
us what you're doing in this file, we can't help you.

> 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.

I'm not going to guess what you mean here. Tell us exactly what you did, 
what it produced, what you expected, why the result didn't work.

Mark