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

[Claus Valka]

Dear Sir,

Thank you very much for your immediate responce.
In order for my text file to succeed it should have
the following format :

a C1 C2 C3 C4
a C5 C6 C7 C7
.
.
.
q

The first line says that we want the atoms with names
C1 C2 C3 C4 (depending on the names according to one's
system).
The last line is also very important because is says
to the make_ndx command to save and quit (something
also that I hadn't included in my file and as a result
the command was running without exiting, yet with the
'a' in front I saw that it had created the indexes I
wanted).

The output for the first three quadraplets is the
following :

[ C1_C4_C7_C10 ]
   1    4    7   10  456  459  462  465  911  914  917
 920 1366 1369 1372
1375 1821 1824 1827 1830 2276 2279 2282 2285 2731 2734
2737 2740 3186 3189
3192 3195 3641 3644 3647 3650 4096 4099 4102 4105 4551
4554 4557 4560 5006
5009 5012 5015 5461 5464 5467 5470 5916 5919 5922 5925
6371 6374 6377 6380
6826 6829 6832 6835
[ C4_C7_C10_C13 ]
   4    7   10   13  459  462  465  468  914  917  920
 923 1369 1372 1375
1378 1824 1827 1830 1833 2279 2282 2285 2288 2734 2737
2740 2743 3189 3192
3195 3198 3644 3647 3650 3653 4099 4102 4105 4108 4554
4557 4560 4563 5009
5012 5015 5018 5464 5467 5470 5473 5919 5922 5925 5928
6374 6377 6380 6383
6829 6832 6835 6838
[ C7_C10_C13_C16 ]
   7   10   13   16  462  465  468  471  917  920  923
 926 1372 1375 1378
1381 1827 1830 1833 1836 2282 2285 2288 2291 2737 2740
2743 2746 3192 3195
3198 3201 3647 3650 3653 3656 4102 4105 4108 4111 4557
4560 4563 4566 5012
5015 5018 5021 5467 5470 5473 5476 5922 5925 5928 5931
6377 6380 6383 6386
6832 6835 6838 6841

>From the online gromacs manual the output I think
should be :
[ C1_C4_C7_C10 ]
   1    4    7   10 
   456  459  462  465
   911  914  917  920
   ...
   ... and so on
Is this really necessary?

I tried to calculate the dihedral distribution for the
first quadraplet and it was calculated without any
error.Can I choose all the quadraplets after the
command :

g_angle -f traj.xtc -s topol.tpr -n index_created.ndx
-b 0 -e (last frame) -type dihedral -od output.xvg

Thank you once again,
Nikos

--- Mark Abraham <Mark.Abraham at anu.edu.au> schrieb:

> 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
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