Support for neutral point mutation #98
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…ato into support_point_mutation
…ato into support_point_mutation
…into parameter_handling
Parameter handling
| self.get_common_core_idx_mol1() + self.dummy_region_cc1.lj_default, | ||
| self.get_common_core_idx_mol2() + self.dummy_region_cc2.lj_default, | ||
| self.get_common_core_idx_mol1(), | ||
| self.get_common_core_idx_mol2(), | ||
| self.psfs["m1"], |
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I don't know if we can remove the self.dummy_region_cc1.lj_default variable, but in my opinion I think it's not necessary since this atom (the lj default atom) is not part of the common core anymore and thus can vary between different ligands
…ato into support_point_mutation
…ato into support_point_mutation
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Point mutations are now fully supported for the CHARMM Force Field in this PR #116 |
A first attempt, to support point mutations of simple RNA/DNA strands. The basic idea is to calculate RBFE between the complex (the double helix solvated in water) and the waterbox (the single strand solvated in water). In this case, there will be no specific small molecule parameters in a
unkfolder. There are a few modifications:system.pyfile: I created a function calledcreate_sdf_filewhich creates a sdf file of the rna/dna from the file provided inwaterbox/step3_input.pdb. It will remove all atoms which are not part of segid RNAA!state.pyfile: if there are no ligand specific folders, TF will not stop from runningmutate.pyfile: Some modifications when the ligand1 (the whole chain RNAA of system 1) is compared to ligand2 (the whole chain RNAA of system 2). It's now ensured that only atoms which are from the same residue are compared, that is currently solved a little bit complicated, but there are some special cases, e.g. there is a residue called GUA which has different atom types (depending on the position of GUA), we now have to ensure that always the same GUA residues are comparedATTENTION Currently some parts are hard-coded, expecting always a chain called RNAA and one called RNAB, while RNAB is always considered to be identical for both systems.