[gmx-users] how to make a index file
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.
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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