Is there any tool or online server where I can prepare a model structure for charged t-RNA with specific amino acid..? I want to use this model further for docking and MD simulation study.
Hi Jaykumar! If your tRNA does not exist in a PDB databank you may create it by yourself using Avogadro as a molecular editor (in Build you may create the structure by adding nucleotides). Then depending on your MD software you can create further files for your simulation. However, for a specific protonation state you will need to add/delete hydrogens where it is needed. Regarding the force field I can suggest you the lates version of AMBER improved for nucleic acids.
If by "charged" you mean charged with an amino acid, if you have a structure of the tRNA, use a molecule viewer/molecular modeling program to bring the amino acid into the appropriate position and set an ester bond between the alpha-carboxylate oxygen and the ribose 3' OH as depicted here:
https://en.wikipedia.org/wiki/Aminoacyl-tRNA#/media/File:Aminoacyl-tRNA.png
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