[gmx-users] Re:Indexing specific atoms

Erik Marklund erikm at xray.bmc.uu.se
Fri Feb 19 11:39:10 CET 2010

shayamra at post.tau.ac.il skrev:
> Hello Parthiban,
> Can you elaborate more on the 'wrong answer'?
> Perhaps the following link can shed some light on the 'wrong' answer:
> http://lists.gromacs.org/pipermail/gmx-users/2009-March/040276.html
> [Deals with g_dist and PBC]
> Regards,
> -Shay
> Quoting parthiban at ncbs.res.in:
>> Hello,
>> Can anyone tell, how to index two specific atoms, (one form protein and
>> one from ligand)
>> eg; 440th atom of protein & 450th atom of small molecule or OED of small
>> molecule.
The format of the index files is simple. You can easily write a script 
to accomplish waht you want, or even do it manually. First you need to 
add the name of the index group,

[ the_name ]

Then follows the list of atoms belonging to the group. If you want the 
440h atom of the protein, then just write 440 plus the number of the 
first atom in the protein. So if your protein starts at atom no 123, 
then its 440 atom will be number 563. Your index group will look 
something like this:

[ the_440th_protein_atom ]

This you can do with the text editor of your choice. Simple as that.

>> My second question is:
>> how to calculate the distance b/w these two atoms.
>> i tried g_dist by including the indexed file with this, but the graph
>> displays a wrong answer.
>> thanks
>> In advance.
>> Parthiban.
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys

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