GROMACS version: version 2018.1
I have used charmm27 to create the itp file which was created using cgenff where both protein and ligand is defined. Later the .gro file was created with all defined atoms, but when i tried to add ions I’m getting atomtype F not found error. which is present in both my itp as well as pdb file.
CHARMM27 (as distributed with GROMACS) does not support CGenFF. Use the CHARMM36 port instead (MacKerell Lab).
F is not a valid atom type in CGenFF. Please give more details about what you’ve done and how you generated the topology.
I have even tried using charmm36 same error, in .itp file as well as .pdb file its showing fluorine. but while running gromacs its showing atomtype not found.
You will need to provide an explicit, step-by-step description of what you’re doing and how you prepared the topology (including all relevant commands and error output). Otherwise, there’s nothing anyone here can do but guess as to the source of the issue.
Protein topology file was created using charmm36. Ligand itp file was created using CGenFF and complex gro file was created according to the instruction given in tutorial. but while adding ions, I am getting error message as Atomtype F not found. when i checked Itp and pdb which was created by CGenFF file fluorine is present. I am not able to understand where I am going wrong.
Nothing in the CHARMM force field or CGenFF (and certainly not via the MacKerell lab’s server) should ever write an atom type of F, so I’m still not understanding. The content of the PDB file is irrelevant; atom types are chemical descriptors while atom names (which are in the coordinate file) can be anything and are not related to this error.
Please upload your ligand .itp file so I can have a look at it.
Hi,
Below i have attached .itp file which was generated from cgenff for which charmm36 ff was used
; Created by cgenff_charmm2gmx.py
[ moleculetype ]
; Name nrexcl
ligand 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ligand rtp ligand q qsum
1 CG2R61 1 ligand C1 1 -0.113 12.011 ;
2 CG2R61 1 ligand C2 2 -0.110 12.011 ;
3 CG2R61 1 ligand C3 3 -0.116 12.011 ;
4 CG2R61 1 ligand C4 4 -0.113 12.011 ;
5 CG2R62 1 ligand C5 5 0.392 12.011 ;
6 CG2R62 1 ligand C6 6 -0.002 12.011 ;
7 CG2R62 1 ligand C7 7 -0.148 12.011 ;
8 OG3R60 1 ligand O8 8 -0.352 15.999 ;
9 CG2R63 1 ligand C9 9 0.699 12.011 ;
10 CG2R62 1 ligand C10 10 -0.490 12.011 ;
11 OG2D4 1 ligand O12 11 -0.416 15.999 ;
12 CG2O1 1 ligand C11 12 0.742 12.011 ;
13 NG2D1 1 ligand N13 13 -0.950 14.007 ;
14 OG2D1 1 ligand O34 14 0.335 15.999 ;
15 NG2D1 1 ligand N14 15 -0.974 14.007 ;
16 CG2O1 1 ligand C16 16 0.583 12.011 ;
17 OG2D1 1 ligand O15 17 0.195 15.999 ;
18 CG321 1 ligand C17 18 0.210 12.011 ;
19 OG301 1 ligand O18 19 -0.394 15.999 ;
20 CG2R61 1 ligand C19 20 0.198 12.011 ;
21 CG2R61 1 ligand C23 21 -0.131 12.011 ;
22 CG2R61 1 ligand C22 22 -0.115 12.011 ;
23 CG2R61 1 ligand C25 23 0.019 12.011 ;
24 CG2R61 1 ligand C24 24 -0.116 12.011 ;
25 CG2R61 1 ligand C21 25 0.030 12.011 ;
26 CG331 1 ligand C20 26 -0.266 12.011 ;
27 CG2O5 1 ligand C26 27 0.392 12.011 ;
28 OG2D3 1 ligand O27 28 -0.460 15.999 ;
29 CG2R61 1 ligand C28 29 0.046 12.011 ;
30 CG2R61 1 ligand C32 30 -0.171 12.011 ;
31 CG2R61 1 ligand C33 31 -0.089 12.011 ;
32 CG2R66 1 ligand C29 32 0.126 12.011 ;
33 FGR1 1 ligand F35 33 -0.210 18.998 ;
34 CG2R61 1 ligand C30 34 -0.089 12.011 ;
35 CG2R61 1 ligand C31 35 -0.171 12.011 ;
36 HGR61 1 ligand H1 36 0.115 1.008 ;
37 HGR61 1 ligand H2 37 0.115 1.008 ;
38 HGR61 1 ligand H3 38 0.115 1.008 ;
39 HGR61 1 ligand H4 39 0.115 1.008 ;
40 HGR62 1 ligand H5 40 0.182 1.008 ;
41 HGA2 1 ligand H6 41 0.090 1.008 ;
42 HGA2 1 ligand H7 42 0.090 1.008 ;
43 HGR61 1 ligand H8 43 0.115 1.008 ;
44 HGR61 1 ligand H9 44 0.115 1.008 ;
45 HGR61 1 ligand H10 45 0.115 1.008 ;
46 HGA3 1 ligand H11 46 0.090 1.008 ;
47 HGA3 1 ligand H12 47 0.090 1.008 ;
48 HGA3 1 ligand H13 48 0.090 1.008 ;
49 HGR61 1 ligand H14 49 0.115 1.008 ;
50 HGR62 1 ligand H15 50 0.181 1.008 ;
51 HGR62 1 ligand H16 51 0.181 1.008 ;
52 HGR61 1 ligand H17 52 0.115 1.008 ;
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 ; CG2R61 CG2R61
1 6 1 ; CG2R61 CG2R62
1 36 1 ; CG2R61 HGR61
2 3 1 ; CG2R61 CG2R61
2 37 1 ; CG2R61 HGR61
3 4 1 ; CG2R61 CG2R61
3 38 1 ; CG2R61 HGR61
4 5 1 ; CG2R61 CG2R62
4 39 1 ; CG2R61 HGR61
5 6 1 ; CG2R62 CG2R62
5 8 1 ; CG2R62 OG3R60
6 7 1 ; CG2R62 CG2R62
7 10 1 ; CG2R62 CG2R62
7 40 1 ; CG2R62 HGR62
8 9 1 ; OG3R60 CG2R63
9 11 1 ; CG2R63 OG2D4
9 10 1 ; CG2R63 CG2R62
10 12 1 ; CG2R62 CG2O1
12 13 1 ; CG2O1 NG2D1
12 14 1 ; CG2O1 OG2D1
13 15 1 ; NG2D1 NG2D1
15 16 1 ; NG2D1 CG2O1
16 18 1 ; CG2O1 CG321
16 17 1 ; CG2O1 OG2D1
18 19 1 ; CG321 OG301
18 41 1 ; CG321 HGA2
18 42 1 ; CG321 HGA2
19 20 1 ; OG301 CG2R61
20 21 1 ; CG2R61 CG2R61
20 25 1 ; CG2R61 CG2R61
21 22 1 ; CG2R61 CG2R61
21 43 1 ; CG2R61 HGR61
22 23 1 ; CG2R61 CG2R61
22 44 1 ; CG2R61 HGR61
23 24 1 ; CG2R61 CG2R61
23 27 1 ; CG2R61 CG2O5
24 25 1 ; CG2R61 CG2R61
24 45 1 ; CG2R61 HGR61
25 26 1 ; CG2R61 CG331
26 46 1 ; CG331 HGA3
26 47 1 ; CG331 HGA3
26 48 1 ; CG331 HGA3
27 28 1 ; CG2O5 OG2D3
27 29 1 ; CG2O5 CG2R61
29 35 1 ; CG2R61 CG2R61
29 30 1 ; CG2R61 CG2R61
30 31 1 ; CG2R61 CG2R61
30 49 1 ; CG2R61 HGR61
31 32 1 ; CG2R61 CG2R66
31 50 1 ; CG2R61 HGR62
32 33 1 ; CG2R66 FGR1
32 34 1 ; CG2R66 CG2R61
34 35 1 ; CG2R61 CG2R61
34 51 1 ; CG2R61 HGR62
35 52 1 ; CG2R61 HGR61
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 38 1
1 8 1
1 10 1
1 40 1
2 5 1
2 7 1
2 39 1
3 6 1
3 36 1
3 8 1
4 37 1
4 7 1
4 9 1
5 36 1
5 38 1
5 10 1
5 40 1
5 11 1
6 37 1
6 39 1
6 9 1
6 12 1
7 36 1
7 8 1
7 11 1
7 13 1
7 14 1
8 39 1
8 12 1
9 40 1
9 13 1
9 14 1
10 15 1
11 12 1
12 40 1
12 16 1
13 18 1
13 17 1
14 15 1
15 19 1
15 41 1
15 42 1
16 20 1
17 19 1
17 41 1
17 42 1
18 21 1
18 25 1
19 22 1
19 43 1
19 24 1
19 26 1
20 41 1
20 42 1
20 23 1
20 44 1
20 45 1
20 46 1
20 47 1
20 48 1
21 24 1
21 26 1
21 27 1
22 25 1
22 45 1
22 28 1
22 29 1
23 43 1
23 26 1
23 35 1
23 30 1
24 44 1
24 28 1
24 29 1
24 46 1
24 47 1
24 48 1
25 43 1
25 27 1
26 45 1
27 44 1
27 45 1
27 34 1
27 52 1
27 31 1
27 49 1
28 35 1
28 30 1
29 32 1
29 50 1
29 51 1
30 34 1
30 52 1
30 33 1
31 35 1
31 51 1
32 49 1
32 52 1
33 50 1
33 35 1
33 51 1
34 50 1
35 49 1
36 37 1
37 38 1
38 39 1
43 44 1
49 50 1
51 52 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 6 5 ; CG2R61 CG2R61 CG2R62
2 1 36 5 ; CG2R61 CG2R61 HGR61
6 1 36 5 ; CG2R62 CG2R61 HGR61
1 2 3 5 ; CG2R61 CG2R61 CG2R61
1 2 37 5 ; CG2R61 CG2R61 HGR61
3 2 37 5 ; CG2R61 CG2R61 HGR61
2 3 4 5 ; CG2R61 CG2R61 CG2R61
2 3 38 5 ; CG2R61 CG2R61 HGR61
4 3 38 5 ; CG2R61 CG2R61 HGR61
3 4 5 5 ; CG2R61 CG2R61 CG2R62
3 4 39 5 ; CG2R61 CG2R61 HGR61
5 4 39 5 ; CG2R62 CG2R61 HGR61
4 5 6 5 ; CG2R61 CG2R62 CG2R62
4 5 8 5 ; CG2R61 CG2R62 OG3R60
6 5 8 5 ; CG2R62 CG2R62 OG3R60
1 6 5 5 ; CG2R61 CG2R62 CG2R62
1 6 7 5 ; CG2R61 CG2R62 CG2R62
5 6 7 5 ; CG2R62 CG2R62 CG2R62
6 7 10 5 ; CG2R62 CG2R62 CG2R62
6 7 40 5 ; CG2R62 CG2R62 HGR62
10 7 40 5 ; CG2R62 CG2R62 HGR62
5 8 9 5 ; CG2R62 OG3R60 CG2R63
8 9 11 5 ; OG3R60 CG2R63 OG2D4
8 9 10 5 ; OG3R60 CG2R63 CG2R62
11 9 10 5 ; OG2D4 CG2R63 CG2R62
7 10 9 5 ; CG2R62 CG2R62 CG2R63
7 10 12 5 ; CG2R62 CG2R62 CG2O1
9 10 12 5 ; CG2R63 CG2R62 CG2O1
10 12 13 5 ; CG2R62 CG2O1 NG2D1
10 12 14 5 ; CG2R62 CG2O1 OG2D1
13 12 14 5 ; NG2D1 CG2O1 OG2D1
12 13 15 5 ; CG2O1 NG2D1 NG2D1
13 15 16 5 ; NG2D1 NG2D1 CG2O1
15 16 18 5 ; NG2D1 CG2O1 CG321
15 16 17 5 ; NG2D1 CG2O1 OG2D1
18 16 17 5 ; CG321 CG2O1 OG2D1
16 18 19 5 ; CG2O1 CG321 OG301
16 18 41 5 ; CG2O1 CG321 HGA2
16 18 42 5 ; CG2O1 CG321 HGA2
19 18 41 5 ; OG301 CG321 HGA2
19 18 42 5 ; OG301 CG321 HGA2
41 18 42 5 ; HGA2 CG321 HGA2
18 19 20 5 ; CG321 OG301 CG2R61
19 20 21 5 ; OG301 CG2R61 CG2R61
19 20 25 5 ; OG301 CG2R61 CG2R61
21 20 25 5 ; CG2R61 CG2R61 CG2R61
20 21 22 5 ; CG2R61 CG2R61 CG2R61
20 21 43 5 ; CG2R61 CG2R61 HGR61
22 21 43 5 ; CG2R61 CG2R61 HGR61
21 22 23 5 ; CG2R61 CG2R61 CG2R61
21 22 44 5 ; CG2R61 CG2R61 HGR61
23 22 44 5 ; CG2R61 CG2R61 HGR61
22 23 24 5 ; CG2R61 CG2R61 CG2R61
22 23 27 5 ; CG2R61 CG2R61 CG2O5
24 23 27 5 ; CG2R61 CG2R61 CG2O5
23 24 25 5 ; CG2R61 CG2R61 CG2R61
23 24 45 5 ; CG2R61 CG2R61 HGR61
25 24 45 5 ; CG2R61 CG2R61 HGR61
20 25 24 5 ; CG2R61 CG2R61 CG2R61
20 25 26 5 ; CG2R61 CG2R61 CG331
24 25 26 5 ; CG2R61 CG2R61 CG331
25 26 46 5 ; CG2R61 CG331 HGA3
25 26 47 5 ; CG2R61 CG331 HGA3
25 26 48 5 ; CG2R61 CG331 HGA3
46 26 47 5 ; HGA3 CG331 HGA3
46 26 48 5 ; HGA3 CG331 HGA3
47 26 48 5 ; HGA3 CG331 HGA3
23 27 28 5 ; CG2R61 CG2O5 OG2D3
23 27 29 5 ; CG2R61 CG2O5 CG2R61
28 27 29 5 ; OG2D3 CG2O5 CG2R61
27 29 35 5 ; CG2O5 CG2R61 CG2R61
27 29 30 5 ; CG2O5 CG2R61 CG2R61
35 29 30 5 ; CG2R61 CG2R61 CG2R61
29 30 31 5 ; CG2R61 CG2R61 CG2R61
29 30 49 5 ; CG2R61 CG2R61 HGR61
31 30 49 5 ; CG2R61 CG2R61 HGR61
30 31 32 5 ; CG2R61 CG2R61 CG2R66
30 31 50 5 ; CG2R61 CG2R61 HGR62
32 31 50 5 ; CG2R66 CG2R61 HGR62
31 32 33 5 ; CG2R61 CG2R66 FGR1
31 32 34 5 ; CG2R61 CG2R66 CG2R61
33 32 34 5 ; FGR1 CG2R66 CG2R61
32 34 35 5 ; CG2R66 CG2R61 CG2R61
32 34 51 5 ; CG2R66 CG2R61 HGR62
35 34 51 5 ; CG2R61 CG2R61 HGR62
29 35 34 5 ; CG2R61 CG2R61 CG2R61
29 35 52 5 ; CG2R61 CG2R61 HGR61
34 35 52 5 ; CG2R61 CG2R61 HGR61
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
6 1 2 3 9 ; CG2R62 CG2R61 CG2R61 CG2R61
6 1 2 37 9 ; CG2R62 CG2R61 CG2R61 HGR61
36 1 2 3 9 ; HGR61 CG2R61 CG2R61 CG2R61
36 1 2 37 9 ; HGR61 CG2R61 CG2R61 HGR61
2 1 6 5 9 ; CG2R61 CG2R61 CG2R62 CG2R62
2 1 6 7 9 ; CG2R61 CG2R61 CG2R62 CG2R62
36 1 6 5 9 ; HGR61 CG2R61 CG2R62 CG2R62
36 1 6 7 9 ; HGR61 CG2R61 CG2R62 CG2R62
1 2 3 4 9 ; CG2R61 CG2R61 CG2R61 CG2R61
1 2 3 38 9 ; CG2R61 CG2R61 CG2R61 HGR61
37 2 3 4 9 ; HGR61 CG2R61 CG2R61 CG2R61
37 2 3 38 9 ; HGR61 CG2R61 CG2R61 HGR61
2 3 4 5 9 ; CG2R61 CG2R61 CG2R61 CG2R62
2 3 4 39 9 ; CG2R61 CG2R61 CG2R61 HGR61
38 3 4 5 9 ; HGR61 CG2R61 CG2R61 CG2R62
38 3 4 39 9 ; HGR61 CG2R61 CG2R61 HGR61
3 4 5 6 9 ; CG2R61 CG2R61 CG2R62 CG2R62
3 4 5 8 9 ; CG2R61 CG2R61 CG2R62 OG3R60
39 4 5 6 9 ; HGR61 CG2R61 CG2R62 CG2R62
39 4 5 8 9 ; HGR61 CG2R61 CG2R62 OG3R60
4 5 6 1 9 ; CG2R61 CG2R62 CG2R62 CG2R61
4 5 6 7 9 ; CG2R61 CG2R62 CG2R62 CG2R62
8 5 6 1 9 ; OG3R60 CG2R62 CG2R62 CG2R61
8 5 6 7 9 ; OG3R60 CG2R62 CG2R62 CG2R62
4 5 8 9 9 ; CG2R61 CG2R62 OG3R60 CG2R63
6 5 8 9 9 ; CG2R62 CG2R62 OG3R60 CG2R63
1 6 7 10 9 ; CG2R61 CG2R62 CG2R62 CG2R62
1 6 7 40 9 ; CG2R61 CG2R62 CG2R62 HGR62
5 6 7 10 9 ; CG2R62 CG2R62 CG2R62 CG2R62
5 6 7 40 9 ; CG2R62 CG2R62 CG2R62 HGR62
6 7 10 9 9 ; CG2R62 CG2R62 CG2R62 CG2R63
6 7 10 12 9 ; CG2R62 CG2R62 CG2R62 CG2O1
40 7 10 9 9 ; HGR62 CG2R62 CG2R62 CG2R63
40 7 10 12 9 ; HGR62 CG2R62 CG2R62 CG2O1
5 8 9 11 9 ; CG2R62 OG3R60 CG2R63 OG2D4
5 8 9 10 9 ; CG2R62 OG3R60 CG2R63 CG2R62
8 9 10 7 9 ; OG3R60 CG2R63 CG2R62 CG2R62
8 9 10 12 9 ; OG3R60 CG2R63 CG2R62 CG2O1
11 9 10 7 9 ; OG2D4 CG2R63 CG2R62 CG2R62
11 9 10 12 9 ; OG2D4 CG2R63 CG2R62 CG2O1
7 10 12 13 9 ; CG2R62 CG2R62 CG2O1 NG2D1
7 10 12 14 9 ; CG2R62 CG2R62 CG2O1 OG2D1
9 10 12 13 9 ; CG2R63 CG2R62 CG2O1 NG2D1
9 10 12 14 9 ; CG2R63 CG2R62 CG2O1 OG2D1
10 12 13 15 9 ; CG2R62 CG2O1 NG2D1 NG2D1
14 12 13 15 9 ; OG2D1 CG2O1 NG2D1 NG2D1
12 13 15 16 9 ; CG2O1 NG2D1 NG2D1 CG2O1
13 15 16 18 9 ; NG2D1 NG2D1 CG2O1 CG321
13 15 16 17 9 ; NG2D1 NG2D1 CG2O1 OG2D1
15 16 18 19 9 ; NG2D1 CG2O1 CG321 OG301
15 16 18 41 9 ; NG2D1 CG2O1 CG321 HGA2
15 16 18 42 9 ; NG2D1 CG2O1 CG321 HGA2
17 16 18 19 9 ; OG2D1 CG2O1 CG321 OG301
17 16 18 41 9 ; OG2D1 CG2O1 CG321 HGA2
17 16 18 42 9 ; OG2D1 CG2O1 CG321 HGA2
16 18 19 20 9 ; CG2O1 CG321 OG301 CG2R61
41 18 19 20 9 ; HGA2 CG321 OG301 CG2R61
42 18 19 20 9 ; HGA2 CG321 OG301 CG2R61
18 19 20 21 9 ; CG321 OG301 CG2R61 CG2R61
18 19 20 25 9 ; CG321 OG301 CG2R61 CG2R61
19 20 21 22 9 ; OG301 CG2R61 CG2R61 CG2R61
19 20 21 43 9 ; OG301 CG2R61 CG2R61 HGR61
25 20 21 22 9 ; CG2R61 CG2R61 CG2R61 CG2R61
25 20 21 43 9 ; CG2R61 CG2R61 CG2R61 HGR61
19 20 25 24 9 ; OG301 CG2R61 CG2R61 CG2R61
19 20 25 26 9 ; OG301 CG2R61 CG2R61 CG331
21 20 25 24 9 ; CG2R61 CG2R61 CG2R61 CG2R61
21 20 25 26 9 ; CG2R61 CG2R61 CG2R61 CG331
20 21 22 23 9 ; CG2R61 CG2R61 CG2R61 CG2R61
20 21 22 44 9 ; CG2R61 CG2R61 CG2R61 HGR61
43 21 22 23 9 ; HGR61 CG2R61 CG2R61 CG2R61
43 21 22 44 9 ; HGR61 CG2R61 CG2R61 HGR61
21 22 23 24 9 ; CG2R61 CG2R61 CG2R61 CG2R61
21 22 23 27 9 ; CG2R61 CG2R61 CG2R61 CG2O5
44 22 23 24 9 ; HGR61 CG2R61 CG2R61 CG2R61
44 22 23 27 9 ; HGR61 CG2R61 CG2R61 CG2O5
22 23 24 25 9 ; CG2R61 CG2R61 CG2R61 CG2R61
22 23 24 45 9 ; CG2R61 CG2R61 CG2R61 HGR61
27 23 24 25 9 ; CG2O5 CG2R61 CG2R61 CG2R61
27 23 24 45 9 ; CG2O5 CG2R61 CG2R61 HGR61
22 23 27 28 9 ; CG2R61 CG2R61 CG2O5 OG2D3
22 23 27 29 9 ; CG2R61 CG2R61 CG2O5 CG2R61
24 23 27 28 9 ; CG2R61 CG2R61 CG2O5 OG2D3
24 23 27 29 9 ; CG2R61 CG2R61 CG2O5 CG2R61
23 24 25 20 9 ; CG2R61 CG2R61 CG2R61 CG2R61
23 24 25 26 9 ; CG2R61 CG2R61 CG2R61 CG331
45 24 25 20 9 ; HGR61 CG2R61 CG2R61 CG2R61
45 24 25 26 9 ; HGR61 CG2R61 CG2R61 CG331
20 25 26 46 9 ; CG2R61 CG2R61 CG331 HGA3
20 25 26 47 9 ; CG2R61 CG2R61 CG331 HGA3
20 25 26 48 9 ; CG2R61 CG2R61 CG331 HGA3
24 25 26 46 9 ; CG2R61 CG2R61 CG331 HGA3
24 25 26 47 9 ; CG2R61 CG2R61 CG331 HGA3
24 25 26 48 9 ; CG2R61 CG2R61 CG331 HGA3
23 27 29 35 9 ; CG2R61 CG2O5 CG2R61 CG2R61
23 27 29 30 9 ; CG2R61 CG2O5 CG2R61 CG2R61
28 27 29 35 9 ; OG2D3 CG2O5 CG2R61 CG2R61
28 27 29 30 9 ; OG2D3 CG2O5 CG2R61 CG2R61
27 29 35 34 9 ; CG2O5 CG2R61 CG2R61 CG2R61
27 29 35 52 9 ; CG2O5 CG2R61 CG2R61 HGR61
30 29 35 34 9 ; CG2R61 CG2R61 CG2R61 CG2R61
30 29 35 52 9 ; CG2R61 CG2R61 CG2R61 HGR61
27 29 30 31 9 ; CG2O5 CG2R61 CG2R61 CG2R61
27 29 30 49 9 ; CG2O5 CG2R61 CG2R61 HGR61
35 29 30 31 9 ; CG2R61 CG2R61 CG2R61 CG2R61
35 29 30 49 9 ; CG2R61 CG2R61 CG2R61 HGR61
29 30 31 32 9 ; CG2R61 CG2R61 CG2R61 CG2R66
29 30 31 50 9 ; CG2R61 CG2R61 CG2R61 HGR62
49 30 31 32 9 ; HGR61 CG2R61 CG2R61 CG2R66
49 30 31 50 9 ; HGR61 CG2R61 CG2R61 HGR62
30 31 32 33 9 ; CG2R61 CG2R61 CG2R66 FGR1
30 31 32 34 9 ; CG2R61 CG2R61 CG2R66 CG2R61
50 31 32 33 9 ; HGR62 CG2R61 CG2R66 FGR1
50 31 32 34 9 ; HGR62 CG2R61 CG2R66 CG2R61
31 32 34 35 9 ; CG2R61 CG2R66 CG2R61 CG2R61
31 32 34 51 9 ; CG2R61 CG2R66 CG2R61 HGR62
33 32 34 35 9 ; FGR1 CG2R66 CG2R61 CG2R61
33 32 34 51 9 ; FGR1 CG2R66 CG2R61 HGR62
32 34 35 29 9 ; CG2R66 CG2R61 CG2R61 CG2R61
32 34 35 52 9 ; CG2R66 CG2R61 CG2R61 HGR61
51 34 35 29 9 ; HGR62 CG2R61 CG2R61 CG2R61
51 34 35 52 9 ; HGR62 CG2R61 CG2R61 HGR61
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
9 10 11 8 2
12 10 13 14 2
16 18 15 17 2
27 23 29 28 2
Dear Gromacs Users,
I am having a similar kind of situation.
I prepared two individual systems using CHARMM-GUI interface.
System 1: PSM lipids with Zeaxanthin molecule
System 2 : DOPC lipids with Zeaxanthin molecule.
Now I wanted to club these systems together.
Now when I am trying to generate the tpr file, gromacs reports an error stating:
Atomtype OSL not found.
And this error is from itp of DOPC.
I checked the ITP file of DOPC lipid and OSL is present.
Following is my topology file:
; Include forcefield parameters
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/forcefield.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/K3I.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/CHL1.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/PSM.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/POT.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/CLA.itp”
#include “…/…/…/…/PROJECT-2/SM-Zeaxanthin/charmm-gui-9945303884/gromacs/toppar/TIP3.itp”
#include “…/…/…/DOPC-Zea-system/charmm-gui-0133839674/gromacs/toppar/DOPC.itp”
[ system ]
; Name
Title
[ molecules ]
; Compound #mols
K3I 1
CHL1 38
PSM 128
POT 12
CLA 12
TIP3 5407
K3I 1
DOPC 128
POT 15
CLA 15
TIP3 5999
Following is the itp file for DOPC:
[ moleculetype ]
; name nrexcl
DOPC 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 NTL 1 DOPC N 1 -0.600000 14.0070 ; qtot -0.600
2 CTL2 1 DOPC C12 2 -0.100000 12.0110 ; qtot -0.700
3 HL 1 DOPC H12A 3 0.250000 1.0080 ; qtot -0.450
4 HL 1 DOPC H12B 4 0.250000 1.0080 ; qtot -0.200
5 CTL5 1 DOPC C13 5 -0.350000 12.0110 ; qtot -0.550
6 HL 1 DOPC H13A 6 0.250000 1.0080 ; qtot -0.300
7 HL 1 DOPC H13B 7 0.250000 1.0080 ; qtot -0.050
8 HL 1 DOPC H13C 8 0.250000 1.0080 ; qtot 0.200
9 CTL5 1 DOPC C14 9 -0.350000 12.0110 ; qtot -0.150
10 HL 1 DOPC H14A 10 0.250000 1.0080 ; qtot 0.100
11 HL 1 DOPC H14B 11 0.250000 1.0080 ; qtot 0.350
12 HL 1 DOPC H14C 12 0.250000 1.0080 ; qtot 0.600
13 CTL5 1 DOPC C15 13 -0.350000 12.0110 ; qtot 0.250
14 HL 1 DOPC H15A 14 0.250000 1.0080 ; qtot 0.500
15 HL 1 DOPC H15B 15 0.250000 1.0080 ; qtot 0.750
16 HL 1 DOPC H15C 16 0.250000 1.0080 ; qtot 1.000
17 CTL2 1 DOPC C11 17 -0.080000 12.0110 ; qtot 0.920
18 HAL2 1 DOPC H11A 18 0.090000 1.0080 ; qtot 1.010
19 HAL2 1 DOPC H11B 19 0.090000 1.0080 ; qtot 1.100
20 PL 1 DOPC P 20 1.500000 30.9740 ; qtot 2.600
21 O2L 1 DOPC O13 21 -0.780000 15.9994 ; qtot 1.820
22 O2L 1 DOPC O14 22 -0.780000 15.9994 ; qtot 1.040
23 OSLP 1 DOPC O12 23 -0.570000 15.9994 ; qtot 0.470
24 OSLP 1 DOPC O11 24 -0.570000 15.9994 ; qtot -0.100
25 CTL2 1 DOPC C1 25 -0.080000 12.0110 ; qtot -0.180
26 HAL2 1 DOPC HA 26 0.090000 1.0080 ; qtot -0.090
27 HAL2 1 DOPC HB 27 0.090000 1.0080 ; qtot 0.000
28 CTL1 1 DOPC C2 28 0.170000 12.0110 ; qtot 0.170
29 HAL1 1 DOPC HS 29 0.090000 1.0080 ; qtot 0.260
30 OSL 1 DOPC O21 30 -0.490000 15.9994 ; qtot -0.230
31 CL 1 DOPC C21 31 0.900000 12.0110 ; qtot 0.670
32 OBL 1 DOPC O22 32 -0.630000 15.9994 ; qtot 0.040
Gromacs is reporting an error at atom number 30 (OSL)
Kindly let me know how can I resolve this .
Thanks in advance