Table of Contents

1. General arguments
2. Model-specific arguments
   1. Protein
   2. DNA
   3. Protein-DNA interactions
3. Other arguments
4. References

The main function of aa_2_cg.jl is to extract structural information from PDB file and it accecpt only one positional argument, the PDB file name.

Many optional arguments can be used to control the output. In the following we divid them into groups of "general arguments", "model-specific arguments" and "other arguments", and describe the available values respectively.

General arguments

Argument	Explanation
-h, --help	show this help message and exit
-v, --verbose	Output more information to the standerd output.
--log	Output information to a log file.
--mmCIF	Use mmCIF format PDB file as input.
--psf	Generate a PSF file.
--cgpdb	Generate a CG PDB file.
--cgconnect	Add CONECT information to the CG PDB (only works with --cgpdb).
--output-name MYMOL	Specify the name for output.

Model-specific arguments

Argument	Explanation
--force-field-protein FF	Force field for protein. FF can be "AICG2+" [^1] or "Clementi" [^2].
--force-field-DNA FF	Force field for DNA. FF can be "3SPN.2C" [^3].
--force-field-RNA FF	Force field for RNA. FF can be "HT" [^4].
-f, --config CONFIG	Force field configuration details. (default: "")
--use-safe-dihedral I	"Safe dihedral potential" [^5], I can be 0) do nothing; 1) $\cos^2(k\theta)$ type (default); 2) remove dihedral potentials with large angles ( $\theta>5\pi/6$ ); 3) $\sin^3(k\theta)$ type.

Protein

Argument	Explanation
-c, --respac RESPAC_FILE	RESPAC [^6] protein charge distribution data.
--aicg-scale I	Scale AICG2+ [^1] local interactions: I can be 0) average; 1) general (default).
--CCGO-contact-scale F	Scaling native contact interaction coefficient. (default: 1.0)

DNA

Argument	Explanation
--3spn-use-5-phos	Use 5'phosphate.
--3spn-param I	Generate 3SPN.2C parameters from library DNA structure. (default: 0)

Protein-DNA interactions

Argument	Explanation
--protein-DNA-Go	Generate parameters for protein-DNA Go-like contact interactions.
--cgRNA-phosphate-Go	Include phosphate in Go-type contact interactions.
-p, --pfm PFM_FILE	Position frequency matrix file for protein-DNA sequence-specific interactions.
--pwmcos	Generate parameters for protein-DNA sequence-specific interactions [^7].
--pwmcos-scale F	Energy scaling factor for PWMcos [^7]. (default: 1.0)
--pwmcos-shift F	Energy shifting factor for PWMcos [^7]. (default: 0.0)
--pwmcos-ns	Generate parameters for protein-DNA sequence-NON-specific interactions [^8].
--pwmcos-ns-ene F	Interaction strength for PWMcos-ns (hydrogen-bond) [^8]. ( default: -1.0)
--patch ITP_FILE	Append (apply patch) to .itp file.

Other arguments

Argument	Explanation
--debug	Show debug output.
--show-sequence	Show sequence of biomolecular chains in PDB.
--test-local-only	TEST: only generate local interaction parameters.

[^1]: Li, W., Wang, W. & Takada, S. PNAS 111, 10550–10555 (2014).

[^2]: Clementi, C., Nymeyer, H. & Onuchic, J. N. J Mol Biol 298, 937–953 (2000).

[^3]: Freeman, G. S., et. al., J Chem Phys 141, 165103 (2014).

[^4]: Hori, N. & Takada, S., J Chem Theory Comput 8, 3384–3394 (2012).

[^5]: Tan, C., Jung, J., Kobayashi, C. & Sugita, Y., J Chem Phys 153, 044110 (2020).

[^6]: Terakawa, T. & Takada, S., J Chem Theory Comput 10, 711–721 (2014).

[^7]: Tan, C. & Takada, S., J Chem Theory Comput 14, 3877–3889 (2018).

[^8]: Niina, T., Brandani, G. B., Tan, C. & Takada, S., PLOS Comput Biol 13, e1005880 (2017). Brandani, G. B., Niina, T., Tan, C. & Takada, S., Nucleic Acids Res 46, 6 (2018).