This force field has been specifically designed to cover most pharmaceutical molecules and is compatible with the traditional AMBER force fields in such a way that the two can be mixed during a simulation. The current implementation of the GAFF force field consists of basic atom types and special atom types. Moreover, since GAFF is totally compatible with the AMBER macromolecular force fields it should prove to be a useful molecular mechanical tool for rational drug design. Especially in binding free energy calculations and molecular docking studies.
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This force field has been specifically designed to cover most pharmaceutical molecules and is compatible with the traditional AMBER force fields in such a way that the two can be mixed during a simulation. The current implementation of the GAFF force field consists of basic atom types and special atom types. Moreover, since GAFF is totally compatible with the AMBER macromolecular force fields it should prove to be a useful molecular mechanical tool for rational drug design.
Especially in binding free energy calculations and molecular docking studies. The Antechamber tool set is designed to allow the rapid generation of topology files for use with the AMBER simulation programs. This is useful in situations where you want to automatically screen a large number of compounds.
Allowing antechamber to calculate charges and atom types automatically for us using GAFF allows it to be included in shell scripts that process a large number of compounds. However, as with any automated system it is not perfect and if you plan on focusing on a single system you should consider manually assigning atom types and carefully validating things.
With Antechamber, one may solve the following problems: Automatically identify bond and atom types Judge atomic equivalence Generate residue topology files Find missing force field parameters and supply reasonable suggestions Remember though that Antechamber is not a replacement for due diligence. You should always closely examine the atom types that Antechamber assigns and verify to yourself that the choices are reasonable. You should never use scientific software in a "Black Box" approach!
In this tutorial we shall use the Antechamber tools with LEaP to create topology and coordinate files for the prescription drug Sustiva Efavirenz. Efavirenz is a human immunodeficiency virus type 1 HIV-1 specific, non-nucleoside, reverse transcriptase RT inhibitor marketed by Bristol Myers Squibb for controlling the progression of HIV infection in humans.
The coordinates of sustiva are associated with a residue called "EFZ" Efavirenz. By all means open it up in VMD and take a look at it. We shall use Antechamber to assign atom types to this molecule and also calculate a set of point charges.
Antechamber is the most important program within the set of Antechamber tools. It can perform many file conversions and can also assign atomic charges and atom types. Depending on its inputs, antechamber executes the following programs all provided with AmberTools : sqm, atomtype, am1bcc, bondtype, espgen, respgen and prepgen.
It will also generate a series of intermediate files all in capital letters. The -o sustiva. The -c bcc option tells antechamber to use the AM1-BCC charge model in order to calculate the atomic point charges while the -s 2 option defines the verbosity of the status information provided by antechamber.
In this case we have selected verbose output 2. So, go ahead and run the above command. AC You should also get a whole series of files written to your directory. INF sqm. AC0 divcon. AC sqm. You can safely delete them. The sqm. We are not interested in the data here except to check that the sqm calculation completed successfully: The last line of your sqm.
This contains the definition of our sustiva residue including all of the charges and atom types that we will load into LEaP to when creating our prmtop and rst7 files.
Migar This can be visualized as basically attaching tutorila spring to each of the solute atoms that connects it to its initial position. Left column contains atom names. Then a iterative function is applied to assign bond types for each valence state in a increasing order of penalty scores. This will give a txt file with two columns in it. In this case we will run steps of minimization without the restraints this time. Each time you release the constraint on heavy atoms slowly.
ANTECHAMBER TUTORIAL PDF
Faushura Xleap will add more hydrogen atoms than we need however all extra hydrogens could be easily deleted. You should check these parameters carefully before running a simulation. We will need to use the Sustiva library file sus. Notice how the volume of our system in angstroms 3 initially decreases as our water box relaxes and reaches and equilibrated density, and thus volume. Here hutorial -i sin-for-resp. For each file, antechamebr is run to get Mulliken charges.
Note, we use the restrt file from the second stage of our minimization tutoorial this contains the final minimized structure. You should check these parameters carefully before running a simulation. Create the necessary topology and coordinate files for non-standard residue First of all the energies, potential and total:. It is possible to choose the entire complex or simply the protein or ligand, to color the structure in various ways, antechamher to choose how it is best represented e. You may have to minimize the system several times. This approach allows antechambed system to rapidly move out of an unfavourable geometry without wild oscillations in the energy.
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