[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
> >> >> >>> --
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> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> SOHAM SARKAR
> >> >> >> Junior Research Fellow
> >> >> >> Department of Chemistry
> >> >> >> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
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