[gmx-users] regarding rmsd calculation of protein

[SHAHEE ISLAM]

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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