Hi all,
I did some work on thise dihedrals for polystyrene, and I simplified
my version now, using also the inspiration from PHE residue.
My problem now is that for the dihedral around the CH2-CH bond in the
inner monomer (PS thus) I define in the rtp
-CH CH2 CH +CH2 gd_17
but in the top fileinstead of
2 9 10 17 gd_17
I get this:
2 9 10 11 (without any parameter).
This make me think that pdb2gmx does not count the dihedral as I
defined it (why?) but puts a "default" dihedral there, without any
parameter. I am right? What would be a solution for that?
My dihedrals are now defined as follows (it helps if you really draw
the molecule):
the entries in the rtp file for first (PS1), inner (PS) and last (PSN) monomer:
[PS1]
[dihedrals]
;in the chain - 3-fold (n=3)
CH3 CH +CH2 +CH gd_17
;around CH-CB - 2-fold (n=2)
CH3 CH CB CG5 gd_1
[PS]
[dihedrals]
;in the chain - 3-fold
CH2 CH +CH2 +CH gd_17
-CH CH2 CH +CH2 gd_17
;around CH-CB - 2-fold
CH2 CH CB CG5 gd_1
[PSN]
[dihedrals]
;in the chain - 3-fold (n=3)
-CH CH2 CH CH3 gd_17
;around CH-CB - 2-fold (n=2)
CH2 CH CB CG5 gd_1
The results for trimer in the top file.
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 8 1 gd_1
1 2 9 10 1 gd_17
2 9 10 11 1
9 10 11 16 1 gd_1
9 10 17 18 1 gd_17
10 17 18 25 1 gd_17
17 18 19 24 1 gd_1
Best regards,
Andrea
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