[gmx-users] make_ndx selection of backbone residues

[Christopher Neale]

Make a group of the "or" selections first, then run an "and" on group 4 and your new group.

I don't exactly remember, but maybe you can do it in one step by simply putting the "& 4" at the end instead of the beginning.

Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of 라지브간디 <rajiv at kaist.ac.kr>
Sent: 13 February 2015 00:15
To: gmx-users at gromacs.org
Subject: [gmx-users] make_ndx selection of backbone residues

Hi gmx,
I would like to know how do I choose the particular residues backbone?  Here I intent to select the only specific residues backbone as following way but i guess i am end up with selecting the protein all atoms in residues.
" 4 &  r 8-226 | r 242-308 | r 320-410 | r 414-502 | r 521-862 | r 873-1058 | r 1069-1345 " (I used this)
  0 System              : 226391 atoms  1 Protein             : 14249 atoms  2 Protein-H           : 11094 atoms  3 C-alpha             :  1347 atoms  4 Backbone            :  4041 atoms  5 MainChain           :  5390 atoms  6 MainChain+Cb        :  6677 atoms  7 MainChain+H         :  6686 atoms  8 SideChain           :  7563 atoms  9 SideChain-H         :  5704 atoms 10 Prot-Masses         : 14249 atoms 11 non-Protein         : 212142 atoms 12 Other               :    36 atoms 13 LIG                 :    36 atoms 14 Water               : 212106 atoms 15 SOL                 : 212106 atoms 16 non-Water           : 14285 atoms 17 Backbone_&_r_8-226_r_242-308_r_320-410_r_414-502_r_521-862_r_873-1058_r_1069-1345: 12493 atoms

I suppose to get the backbone selection residues less than backbone (4041 atoms) but it comes 12493 which is close to protein all atoms as i believe i selected the protein all atoms? If so, how do I only select those residues backbone atoms?
Appreciated for your info. Thanks





--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.