[gmx-users] Help with make_ndx and

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 21 17:17:04 CET 2002

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

there is also some online help in make_ndx

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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