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 ...

In earlier post we saw how we create pdb files for the structures we want to consider for multi component molecular dynamics analysis. So now we have say PDB files for four structures - an aldehyde, nitrile, amine and a phenol molecule. Now, In the first step we generate the prepin files for all these molecules by  using: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 Here the molecules are neutral in nature. If you are working with ionic systems you need to add -nc flag in the end followed by charge of the moelcule. So, if the moelcule has +1 charge, the command will be: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc 1 If it is -1, command is: $AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo prepi -c bcc -s 2 -nc -1 If you have followed earlier preocedure properly then your prepin file should be created in no time. You can see some lines of a prepin fil...