[gmx-users] How to use the index.ndx when running rms?

[ZHANG Cheng]

Dear All,
After a few tests, I finally got it.


Actually, the command line below does NOT generate a new set of group. 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
Instead, it outputs ALL the 18 groups, each group contains its relevant atom numbers.


After reading http://biophysics.med.jhmi.edu/~yliu120/tutorials.html
It says: "If the index file you provide only contains one index group. Then the Gromacs program will not ask you for a choice of index groups since you only provide one to it."


So I opened my initial .gro file, check the necessary numbers belong to my protein. Based on this information, I deleted unnecessary groups and numbers in the index.ndx file.


Then run the command with "-n" option:
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n index.ndx


And I successfully got the .xvg file.




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Mon, Aug 14, 2017 11:50 PM
To:  "ZHANG Cheng"<272699575 at qq.com>; "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; 

Subject:  Re: How to use the index.ndx when running rms?



Hi Justin,
Thank you. I added "-n index.ndx" to my rms command, but still got "Cannot read from input" error:


Command line:
  gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd_noPBC.xvg -tu ns -n index.ndx


Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Reading file md_0_1.tpr, VERSION 5.1.1 (single precision)
Select group for least squares fit
Group     0 (         System) has 127073 elements
Group     1 (        Protein) has  8850 elements
Group     2 (      Protein-H) has  4351 elements
Group     3 (        C-alpha) has   645 elements
Group     4 (       Backbone) has  1935 elements
Group     5 (      MainChain) has  2785 elements
Group     6 (   MainChain+Cb) has  3194 elements
Group     7 (    MainChain+H) has  3816 elements
Group     8 (      SideChain) has  5034 elements
Group     9 (    SideChain-H) has  1566 elements
Group    10 (    Prot-Masses) has  8850 elements
Group    11 (    non-Protein) has 118223 elements
Group    12 (          Water) has 117684 elements
Group    13 (            SOL) has 117684 elements
Group    14 (      non-Water) has  9389 elements
Group    15 (            Ion) has   539 elements
Group    16 (             NA) has   155 elements
Group    17 (             CL) has   384 elements
Group    18 ( Water_and_ions) has 118223 elements
Select a group: Select a group: Select a group: 
-------------------------------------------------------
Program gmx rms, VERSION 5.1.1
Source code file: /dev/shm/tmp.PwtfSrm0uJ/gromacs-5.1.1/src/gromacs/topology/index.cpp, line: 917


Fatal error:
Cannot read from input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------







------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Mon, Aug 14, 2017 11:09 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; 
Cc:  "ZHANG Cheng"<272699575 at qq.com>; 
Subject:  How to use the index.ndx when running rms?



Dear Gromacs,
After running 
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.


Then I run 
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in the same folder.


So how to use the index.ndx when running rms?


Thank you.


Yours sincerely
Cheng