Guide to fetch XFF parameters with GENXFF

Note: currently, genxff can only be run on a Linux x86 machine!

Write a config file for genxff

An example config file example.config:

​x
input:
    mol: ligand.sdf    #required, input mol file, supported format [mol, sdf, mol2]
    charge: char_file.chg   #optional, partial charge file 
    mol_name: lig   #optional, ligand name in the output file

output:
    amber: amber_out_name #output: amber_out_name.mol2, amber_out_name.frcmod, amber_out_name_leaprc.dat
    charmm: charmm_out_name #output: charmm_out_name.pdb, charmm_out_name.prm, charmm_out_name.rtf
    gromacs: gromacs_out_name #output: gromacs_out_name.pdb, gromacs_out_name.top

config:
    revise_charge_precision: True
    use_antechamber_for_charge: False

amber: /mnt/workflow/amber20 #amber home

Fetch XFF3.0 parameters with genxff

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genxff --config example.config

Detailed explanation of config file for genxff

Here is a complete version of the config template. You can also obtain it by running

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genxff --dump_config template.config

input:

mol: path to the input ligand file (currently only support mol, sdf, and mol2 format.)

charge: path to the partial charge file

Currently, we support three types of partial charge file

1. Mol2 format with partial charges in it. For example, a mol2 file obtained with antechamber using "-c bcc" option.

2. A single column charge file (.chg).

E.g.

xxxxxxxxxx
-0.01
0.02
-0.03
...

3. A double column charge file (.chg). The first column is the atom index starting from 1 and the second column is the partial charges.

E.g.

xxxxxxxxxx
1 -0.01
2 0.02
3 -0.03
...

mol_name: residue name in the output file

output: (can choose all of them or any of the format combinations)

amber/charmm/gromacs: output file name for amber/charmm/gromacs format. Output files for the designated format will be generated in the current working directory.

config:

revise_charge_precision: whether to adjust atomic partial charges so that their sum matches exactly the net charge of the molecule. Usually True.

use_antechamber_for_charge: whether to use antechamber to calculate AM1BCC charges, usually False if a charge file is provided.

amber: path to amberhome if you want to use antechamber.