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Hello, thanks for this useful software! As used in this paper, I would like to perform CG simulation of IDP using a combination of AICG2+ and HPS. I read the wiki and the test code (genesis_cg_tool/test/NHP_IDR.toml) as a reference to set up the coarse-grained file.

Question

1. I'm not familiar with the gromacs file format, but should I specify any options other than those shown below?
2. Is it enough to just change the charge of .itp file without renaming atomtype if I want to change the charge of particular particle?

Assumptions

• IDP has 738 residues, non-IDR is 1 to 267 and IDR is 268 to 738.
• I would like to simulate the non-IDR part using AICG2+ and the IDR part using HPS.

Method

1. Prepare the IDP all-atom pdb file (aa.pdb).
2. Write a toml file (idr.toml) that specifies the IDR.

[ IDR ]
HPS_region = "268 to 738"

3. Specify idr.toml and execute aa_2_cg.jl.

$ /opt/genesis/src/analysis/cg_tools/src/aa_2_cg.jl aa.pdb -f idr.toml

Results

• The following files are generated.
  • aa_cg.gro
  • aa_cg.itp
  • aa_cg.top
• [ angles ], [ dihedrals ], and [ pairs ] in the generated itp file (aa_cg.itp) did not contain IDRs as expected.
• Also, the [ cg_IDR_HPS_region ] item was added.

[ cg_IDR_HPS_region ] ; IDR HPS model 
;        i to          j
         268           738

Thank you.