[gmx-users] regarding rmsd calculation of protein

[SHAHEE ISLAM]

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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