[gmx-users] how to make a index file

Justin Lemkul jalemkul at vt.edu
Thu Sep 12 14:51:42 CEST 2013

On 9/11/13 11:33 PM, aixintiankong wrote:
> i want to analyze the change of secondary structure of the mainchian frome
> residue 20 to residue 60. so i want to make a index file that only contain
> the maninchian+H from residue 20 to residue 60.  i have inputed the command "
> make_ndx -f em.pdb -o index.ndx", but i don't kown how to do next . what
> should i input ? thank you very much!

A good place to start is to type "help" at the prompt to see full syntax 
information and examples.  In this case, creating the group is very easy:

7 & r 20-60

This tells make_ndx to merge (using &) the common parts of group 7 (MainChain+H) 
and residues 20-60.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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