Adventures in Computational Chemistry

Sometimes you totally fail to go ahead with the prepin and frcmod files you have generated from the newly generated PDB file even after you follow the procedure given in previous two posts. And you keep wondering? In such a case you need a more detailed procedure. First take a look at the pdb file. For example: Here is one such pdb file generated from the gabedit that troubled me for some time. --------------- HEADER    PROTEIN COMPND    UNNAMED AUTHOR    GENERATED BY GABEDIT 2.3.8 at Tue Jul 26 16:53:48 2011 ATOM  1      C   C     1       -2.907  -0.997  -0.385  1.00  300.00          C 0.0000   ATOM  2      N   N     1       -2.060  -0.981  -1.189  1.00  300.00 ...

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...