Open wagleswapnil opened 11 months ago
I'm also struggling to understand this section about dihedral.
Is there some detailed manual related to this? Or could you please point me to certain block of pmx
code?
Thanks a lot.
The dihedrals are constructed here: https://github.com/deGrootLab/pmx/blob/e6d62580df7374c24e3056db5142517b8475daba/src/pmx/ligand_alchemy.py#L2509
Hi, I generated a hybrid topology of two ligands, the [ dihedrals ] section of the hybrid topology looks like this: [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 10 9 3 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 3 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 8 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 10 9 8 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 11 2 3 1 180 24.7411728 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 3 1 180 0 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 23 1 180 15.6141438 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD) 1 11 2 23 1 180 0 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD) 2 3 4 12 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C11x (AAAA->DDAA) 2 3 4 12 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C11x (AAAA->DDAA) ....
The dihedrals for almost all the pairs are defined twice. So, I have 2 questions about this [ dihedrals ] output:
ifdef LIGAND_A
1 10 9 3 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 3 1 180 0 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 8 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 10 9 8 1 180 0 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 11 2 3 1 180 24.7411728 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 3 1 180 0 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD) ....
endif
ifdef LIGAND_B
1 10 9 3 1 180 0 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 3 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 8 1 180 0 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 10 9 8 1 180 15.3215155 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 11 2 3 1 180 0 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 3 1 180 24.7411728 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 23 1 180 0 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD) 1 11 2 23 1 180 15.6141438 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD) ....
endif
ifdef LIGAND_AB
1 10 9 3 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 3 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C3x (AAAA->DDDD) 1 10 9 8 1 180 15.3215155 2 180 0 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 10 9 8 1 180 0 2 180 15.3215155 2 ; C1x C10x C9x C8x (AAAA->DDDD) 1 11 2 3 1 180 24.7411728 2 180 0 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 3 1 180 0 2 180 24.7411728 2 ; C1x N1x C2x C3x (AAAA->DDDD) 1 11 2 23 1 180 15.6141438 2 180 0 2 ; C1x N1x C2x H2x (AAAA->DDDD) 1 11 2 23 1 180 0 2 180 15.6141438 2 ; C1x N1x C2x H2x (AAAA->DDDD) 2 3 4 12 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C11x (AAAA->DDAA) 2 3 4 12 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C11x (AAAA->DDAA) 2 3 4 18 1 180 4.8669776 2 180 0 2 ; C2x C3x C4x C14x (AAAA->DDAA) 2 3 4 18 1 180 0 2 180 0.48669776 2 ; C2x C3x C4x C14x (AAAA->DDAA) ...
endif