[gmx-users] regarding rmsd calculation of protein
SHAHEE ISLAM
islamshahee at gmail.com
Thu May 24 07:43:43 CEST 2018
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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