[gmx-users] regarding rmsd calculation of protein
SHAHEE ISLAM
islamshahee at gmail.com
Thu May 24 08:21:35 CEST 2018
thank you so much for your continuous help.
On 5/24/18, Soham Sarkar <soham9038 at gmail.com> wrote:
>>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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