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Generating a structure PDB file using Gabedit

If Gabedit is installed and functioning on your system, type gabedit  in terminal.
Gabedit will open and you can find an option "Geometry" in the tool bar.

Select "Geometry"--> "Draw"

After some trials and playing you will finally learn how to generate a structure.
Once your structure is ready, you need to set the atom types and charges.
For this click on "M" button in the top left of the "Draw Geometry" window and select options as:
M-->"Set"--> "Atom Type & charge using PDB template"
Here if you use "Atom Types using connection types", it helps.
You can check if the atom type and charge has been set according to the amber requirements by an indirect method. Try to run a quick MM calculation.

Run MM calculations by clicking:

"M"-->Molecular Mechanics-->optimization

It may sometimes end up with a pop up window that suggests that either atom type or charge is not set. If that is case you need to can go back to previous step and again try to set atom type and charge.

Settling this problem of atom types and charge is very important.  Otherwise in further steps, amber gives you hard time recognizing your PDB file properly.


OnceIf the issue of atom type and charge is resolved, run a quick MM and save this geometry as a pdb file.
This newly created pdb file is the one which we will need to use in next step.

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