Using Antechamber

% cd ligand_setup % cp ../TAZ.pdb . Now we have a complete structure for TAZ that can be used by antechamber to produce all the necessary files and parameters for simulation. This pdb file will be used ONLY as input to antechamber, since the coordinates from the Xray structure are more appropriate for our modeling attempt. When the necessary input files and parameters are produced by antechamber, leap will be able to fill in the atoms and bonding information that is missing from the Xray pdb file. Leap will need:

A topology file such as an amber prep file to indicate bonding information, atom types, charges, and initial geometry
Parameters for bonds, angles, dihedrals, impropers and vdW interactions for atom types that are not in the standard force field files.
Charges for atoms

The following command will produce the necessary information for the as yet unknown molecule tazobactam:

% antechamber -i TAZ.pdb -fi pdb -o TAZ.mol2 -fo mol2 -c bcc -s 2

-i: input file name
-fi: format of the input file
-o: output file name
-fo: output file format
-c: charge method
-s: level of verbosity of output

Now check for missing parameters and create a frcmod file containing any missing parameters that can be found. Watch for messages about parameters that may be still missing or of questionable quality in the current model.

% parmchk -i TAZ.mol2 -f mol2 -o TAZ.frcmod

Go on to Using Leap

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