[gmx-users] how to make index file for a complex which is composed of protein and a phosphotyrosine ligand

[Justin Lemkul]

On 1/31/18 6:38 AM, farial tavakoli wrote:
> Dear gmx users
> I need to calculate the energy binding of my complex, composed protein and a phosphotyrosine ligand, using g_mmpba, but when I wanna make an index file by this command:gmx make_ndx -f md_0_1.gro -o index.ndxand type :splitch 1 in order to separate the protein and phosphotyrosine ligand , face to this elements:
> Group     0 (         System) has 67577 elements
> Group     1 (        Protein) has  5290 elements
> Group     2 (      Protein-H) has  2631 elements
> Group     3 (        C-alpha) has   328 elements
> Group     4 (       Backbone) has   984 elements
> Group     5 (      MainChain) has  1310 elements
> Group     6 (   MainChain+Cb) has  1619 elements
> Group     7 (    MainChain+H) has  1624 elements
> Group     8 (      SideChain) has  3666 elements
> Group     9 (    SideChain-H) has  1321 elements
> Group    10 (    Prot-Masses) has  5290 elements
> Group    11 (    non-Protein) has 62287 elements
> Group    12 (          Other) has    48 elements
> Group    13 (            TP2) has    48 elements
> Group    14 (             NA) has    11 elements
> Group    15 (          Water) has 62228 elements
> Group    16 (            SOL) has 62228 elements
> Group    17 (      non-Water) has  5349 elements
> Group    18 (            Ion) has    11 elements
> Group    19 (            TP2) has    48 elements
> Group    20 (             NA) has    11 elements
> Group    21 ( Water_and_ions) has 62239 elements
> Group    22 ( Protein_chain1) has  5204 elements
> Group    23 ( Protein_chain2) has    86 elements
>
> Group 23 is my ligand but without phosphotyrosine groups. Groups 13 & 19 are phosphotyrosine groups. I dont know how I can obtain my ligand with its ohosphotyrosine groups.is there anyone can help me?

Merge the two groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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