[gmx-users] How to generate proper index files...

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 1 08:57:00 CEST 2003

On Tue, 2003-04-01 at 02:44, curtchr1 at iit.edu wrote:
> Hello all,
> I am currently trying to generate an index file for a two component protein,
> two component as in I have two separate ITP files for the dimers that compose
> the protein.  When I generate the index file from the .gro file, which does
> not have any syntax to differentiate between the dimers of the protein,
> I get, as expected, an index file for PROTEIN, not for two separate units.
>  How might I overcome this?  
use make_ndx
then select the residues,if you have residue 1-230 in chain A and
231-320 in chain B you type

r 1-230
r 231-320

this gives you two new groups that you can rename with
name 17 chainA
name 18 chainB

(numbers may differ)
> Thanks for the help.
> -Chris Curtis
> Illinois Institute of Technology
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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