[gmx-users] regarding rmsd calculation of protein

Soham Sarkar soham9038 at gmail.com
Thu May 24 07:45:44 CEST 2018


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
> >> >> >>> --
> >> >> >>> Gromacs Users mailing list
> >> >> >>>
> >> >> >>> * Please search the archive at http://www.gromacs.org/
> >> >> >>> Support/Mailing_Lists/GMX-Users_List before posting!
> >> >> >>>
> >> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >> >>>
> >> >> >>> * For (un)subscribe requests visit
> >> >> >>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or
> >> >> >>> send a mail to gmx-users-request at gromacs.org.
> >> >> >>>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> SOHAM SARKAR
> >> >> >> Junior Research Fellow
> >> >> >> Department of Chemistry
> >> >> >> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
> >> >> >> --
> >> >> >> Gromacs Users mailing list
> >> >> >>
> >> >> >> * Please search the archive at
> >> >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> >> >> >> posting!
> >> >> >>
> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >> >>
> >> >> >> * For (un)subscribe requests visit
> >> >> >>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or
> >> >> send
> >> >> >> a
> >> >> >> mail to gmx-users-request at gromacs.org.
> >> >> >>
> >> >> >
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
> >> >> * Please search the archive at
> >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> >> posting!
> >> >>
> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >>
> >> >> * For (un)subscribe requests visit
> >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> >> send a mail to gmx-users-request at gromacs.org.
> >> >>
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > * For (un)subscribe requests visit
> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a
> >> > mail to gmx-users-request at gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a
> > mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list