[gmx-users] regarding rmsd calculation of protein

[Soham Sarkar]

It is any .gro file of your system
You can make index file after final md

On Thu, 24 May 2018, 10:37 am SHAHEE ISLAM, <islamshahee at gmail.com> wrote:

> you have mention here em.gro,i think it is a gro file of
> equilibration.can i make the index file after production run to
> calculate rmsd.
>
> On 5/23/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> > thank you so much for your quick reply.
> >
> > On 5/23/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> >> 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
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