[gmx-users] regarding rmsd calculation of protein

[Soham Sarkar]

Put L(small)
It will give the residue number

On Thu, 24 May 2018, 11:00 am SHAHEE ISLAM, <islamshahee at gmail.com> wrote:

> after giving this command
> make_ndx -f em.gro -o index.ndx
> nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>  'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>  't': atom type   |   'keep' nr        'splitat' nr    'h': help
>  'r': residue         'res' nr         'chain' char
>  "name": group        'case': case sensitive           'q': save and quit
>  'ri': residue index
> these all options are shown on the screen.
> but when i am giving
> > |
>
>
> Syntax error: "|"
> can you please tell me what should i give.
>
>
>
>
> On 5/24/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> > 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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