GROMACS version: 2022
GROMACS modification: No
Hi,
I am trying to build an octanoic acid/octanoate bilayer.
I have used cgenff to generate .itp files for both of these fatty acids but I am struggling understand how to incorporate them into the .rtp and .hbd files in the charmm36 ff I am using.
To construct the bilayer I have been trying to start with the lauric acid bilayer first and trim back the chains to make C8.
my .itp looks like:
[ moleculetype ]
; name nrexcl
OCT 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG321 1 OCT C1 1 -0.281 12.0110 ; qtot -0.281
2 CG321 1 OCT C2 2 -0.179 12.0110 ; qtot -0.460
3 CG321 1 OCT C3 3 -0.180 12.0110 ; qtot -0.640
4 CG321 1 OCT C4 4 -0.179 12.0110 ; qtot -0.819
5 CG321 1 OCT C5 5 -0.181 12.0110 ; qtot -1.000
6 CG321 1 OCT C6 6 -0.177 12.0110 ; qtot -1.177
7 CG331 1 OCT C7 7 -0.273 12.0110 ; qtot -1.450
8 CG2O3 1 OCT C8 8 0.620 12.0110 ; qtot -0.830
9 OG2D2 1 OCT O1 9 -0.760 15.9994 ; qtot -1.590
10 OG2D2 1 OCT O2 10 -0.760 15.9994 ; qtot -2.350
11 HGA2 1 OCT H1 11 0.090 1.0080 ; qtot -2.260
12 HGA2 1 OCT H2 12 0.090 1.0080 ; qtot -2.170
13 HGA2 1 OCT H3 13 0.090 1.0080 ; qtot -2.080
14 HGA2 1 OCT H4 14 0.090 1.0080 ; qtot -1.990
15 HGA2 1 OCT H5 15 0.090 1.0080 ; qtot -1.900
16 HGA2 1 OCT H6 16 0.090 1.0080 ; qtot -1.810
17 HGA2 1 OCT H7 17 0.090 1.0080 ; qtot -1.720
18 HGA2 1 OCT H8 18 0.090 1.0080 ; qtot -1.630
19 HGA2 1 OCT H9 19 0.090 1.0080 ; qtot -1.540
20 HGA2 1 OCT H10 20 0.090 1.0080 ; qtot -1.450
21 HGA2 1 OCT H11 21 0.090 1.0080 ; qtot -1.360
22 HGA2 1 OCT H12 22 0.090 1.0080 ; qtot -1.270
23 HGA3 1 OCT H13 23 0.090 1.0080 ; qtot -1.180
24 HGA3 1 OCT H14 24 0.090 1.0080 ; qtot -1.090
25 HGA3 1 OCT H15 25 0.090 1.0080 ; qtot -1.000
[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 8 1
1 11 1
1 12 1
2 3 1
2 13 1
2 14 1
3 4 1
3 15 1
3 16 1
4 5 1
4 17 1
4 18 1
5 6 1
5 19 1
5 20 1
6 7 1
6 21 1
6 22 1
7 23 1
7 24 1
7 25 1
8 9 1
8 10 1
Does anyone have any suggestions or better ideas on how to attack this?