[gmx-users] regarding rmsd calculation of protein

[Soham Sarkar]

Do proper indexing of each chain
> make_ndx -f em.gro -o index.ndx
>l (shows total residue with number)
>ri ( give numbers for residue number of each chain)
>rename them as Chain_A and Chain_B
>v (shows the newly indexed file)
>q (save)
Now your index has two chain seperated

On Wed, May 23, 2018 at 5:54 PM, SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> hi,
> i have two protein in my gro file.when i am calculating rmsd by this
> command
> g_rms -s dynamic.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
>  this options are coming
> Group     0 (         System) has 12059 elements
> Group     1 (        Protein) has   566 elements
> Group     2 (      Protein-H) has   566 elements
> Group     3 (        C-alpha) has     0 elements
> Group     4 (       Backbone) has     0 elements
> Group     5 (      MainChain) has     0 elements
> Group     6 (   MainChain+Cb) has     0 elements
> Group     7 (    MainChain+H) has     0 elements
> Group     8 (      SideChain) has   566 elements
> Group     9 (    SideChain-H) has   566 elements
> Group    10 (    Prot-Masses) has   566 elements
> Group    11 (    non-Protein) has 11493 elements
> Group    12 (          Other) has 11493 elements
> Group    13 (              W) has 11477 elements
> Group    14 (            ION) has    16 elements
> for this reason i am able to calculate the rmsd of two protein
> together by selecting 1.
> but i want to calculate the rmsd of the protein individualy.how i will do
> this.
> My .gro file consist of atom no 1 to 283 for protein1 and atom no 284
> to 566 for protein2.
> thanking you
> shahee islam
> university of calcutta
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-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY