[gmx-users] Help with make_ndx and

[Peter Ahlström]

Note that the numbering of atoms starts at 0 [as in C-programming loops]  and not on 1 [as in fortran programming loops] so there is a small 
difference of numbering (at least as I know from gromacs-2.x) 

Peter Ahlström 
School of engineering      Ph +46-33-17 46 75 
Borås University College   Fax +46-33-16 40 08 
SE-501 90 Borås            peter.ahlstrom at hb.se 
Sweden 


<<< feenstra at chem.vu.nl 25/2 12:17   >>>
David van der Spoel wrote:
> 
> On Thu, 21 Feb 2002, Giorgos Karvounis wrote:
> 
> >My name is Giorgos and i am a new Gromacs user. My problem is that i
> >need to extract and follow the coordinates of a specific aton in a
> >protein (e.g C1) or a group (e.g. carbonyl) but i'm not comfortable with
> >the index.ndx or make_ndx command... Any help will highly appreciated!
> Say you want the carbonyl carbon in residue 34 in your protein:
> 
> make_ndx -f conf.gro
> >r 34 & a C
> >q
> 
> there is also some online help in make_ndx

Additionally, the .ndx file format is terribly easy. It is simply
a line with the name of a group of atoms and then a (number of) line(s)
with the numbers of these atoms. For example, David's example input to
make_ndx could produce an index.ndx file like this:

[ 34-CA ]
152

Which simply says that the group named '34-CA' consisists of atom
number 152 in your conf.gro file... If you can read the conf.gro file,
you can find the atom numbers yourself, sometimes that is easier 
than using make_ndx...

Anyway, good luck!


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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