[gmx-users] regarding rmsd calculation of protein

[SHAHEE ISLAM]

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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>