[gmx-users] regarding rmsd calculation of protein

Soham Sarkar soham9038 at gmail.com
Thu May 24 08:15:02 CEST 2018


>Selecting two chains at a time is of no work because each chain behave
differently which needs to be adressed
>Renaming process
name 15 Chain_A
Then press q to save

On Thu, 24 May 2018, 11:26 am SHAHEE ISLAM, <islamshahee at gmail.com> wrote:

> Really thank you so much for your reply.
> can i select the two chain at a time.because both protein contain 120
> amino acid respectively.
> then
> > ri 1-120
>
> Found 262 atoms with resind.+1 in range 1-120
>
>  15 r_1-120             :   262 atoms
>
> > rename Chain_A
>
> Found 0 atoms with residue names ENAME CHAIN_A
> Group is empty
>
>
> On 5/24/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> > You should give like ri 1-120
> >
> > On Thu, 24 May 2018, 11:14 am SHAHEE ISLAM, <islamshahee at gmail.com>
> wrote:
> >
> >> yes its working.
> >> now
> >> >ri ( give numbers for residue number of each chain)
> >> i have 120 amino acids of two protein each.
> >> when i am giving
> >> > ri 120
> >>
> >>
> >>  15 r_120               :     2 atoms
> >> should i give this in the way.
> >>
> >> On 5/24/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> >> > 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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> >> >> >> >>
> >> >> >> >
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