Hi everyone,
I'm having trouble figuring out which columns represent the charge, sigma, and epsilon values in the commonly available Generalized Amber Force Field file gaff.dat (see attachment or search Google for "gaff.dat").
I've come across posts in amber forums saying "it should follow the param9x.dat format". However, I am unable to pattern match my way into figuring out the gaff.dat file.
I'm specifically interested in the charge, sigma, epsilon parameters needed for running a Lennard-Jones calculation.
Thank you for helping me with such a mundane task.
In gaff.dat, look for the section that starts with "MOD4". It lists the atom types, then two numbers. These are the Lennard-Jones parameters Rmin/2 and epsilon. Note that Rmin/2 is NOT the same as sigma -- it is sigma * the sixth root of 2 (see http://ambermd.org/vdwequation.pdf for more details here).
However, there are no charges in gaff.dat. In fact, there are no charges in any parameter file shipped with Amber. Instead, these charges are found in the residue template libraries (look for the .lib files in $AMBERHOME/dat/leap/lib).
For ligands you parametrize with gaff, you typically use antechamber to generate a library template (typically a mol2 file) which contains the charges and atom types for each of the atoms (the charges being derived from a quantum mechanical calculation). You can find more information on Amber file formats here: http://ambermd.org/formats.html
I would also suggest consulting the Amber mailing list in the future for questions like these, since Amber-related questions get answered much more quickly there.
find the file $AMBERHOME/dat/leap/parm/gaff.dat
Find "MOD4". After that line, there are VdW radius and epsilon for each atom type. The citation is also there.
Hi,
Thank you Xiaoquan and Jason for pointing out that MOD4 contains the vdw and epsilon for each atom type. Much appreciated.
Hassan
Thank you all very much for introducing the structure of .dat file in amber.
And now we can use gaff2.dat.
Hi,
I want to use AMBER Force Field as energy function. Will it be ok if I take the parameter from the following files for protein?
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