Problem in energy minimization ,no default proper Dih. Types

User discussions
1

GROMACS version: latest
GROMACS modification: Yes/No
Here post your question
I have some query like

After making a peptide in discovery studio – D amino acid

  1. I did some changes in the rtp files and hdb files (i did rename the pdb file according to rtp file, but i see changed structure after renaming it so i avoid this and did vice versa by renaming the residue name in rtp entry of D amino acid )

2)The rtp file of the ff basically have the DLEU residue which couldn’t recognize the residue as in pdb D-Leucine was named as DLE so i changed it to

DLEU -> DLE

  1. hdb file of the Charmm36 force field do not have the hydrogen data for D amino acid so i copied the L amino acid and rename it to D amino acid (like LEU->DLE after copying the hydrogen data)

4)And last thing i did was updating residue database file by adding DLE as Protein and all other D amino acid as Protein

After that my error was solved and pdb2gmx executed flawlessly.

While doing the energy minimization step in gromacs package it gives me following error
ERROR 1[file topol.top, line 609]:
No default proper Dih. types
Then after some lines
Fatal error:
There was 1 error in input files

#is it the correct way of modifying forcefield
#how to solve the error ?

Please help

2

Are you using the latest (July 2020) version of CHARMM36? There should be no missing dihedrals. If you can tell me the atom types (in order) of the missing interaction, I will look into it.

3

Yes I am using the latest CHARMM36 (July 2020)
In topology file the 609 line corresponds to
21 36 38 40 9
Which is specified as
CTD1( of DLE)- C (of DLE)- NH1 ( VAL)- CT1(VAL)
in [atom] directive in topol.top
And in pdb it is given as

C ( of DLE)- 2HD2 (of DLE )- N ( VAL)- C(VAL)

is this what you are asking for ?

Thanks

4

Add

     CTD1       C      NH1     CT1      9     0.000000     6.694400     1
     CTD1       C      NH1     CT1      9   180.000000    10.460000     2

to ffbonded.itp under [dihedraltypes]. I’ll make sure this is fixed for the next release. I thought it already had, sorry.

1 Like
5

Thanks a lot

6

Hi, I had the same error for a small molecule (Salicylate) that I added to the most recent charmm36ff. I used methylbenzoate (MBOA) as my template as they are similar, and I was able to generate the .itp file for Salicylate using gmx pdb2gmx without error. I modified merged.rtp, and merged.hdb to get it to work, however when running grompp I get the error:

ERROR 1 [file sal.itp, line 125]:
No default Proper Dih. types

(from sal.itp, line 125 bolded)
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
4 1 2 3 9
12 1 2 3 9
2 1 4 5 9
2 1 4 6 9
12 1 4 5 9
12 1 4 6 9
2 1 12 10 9
2 1 12 13 9
4 1 12 10 9
4 1 12 13 9
1 4 5 14 9
1 4 5 15 9
6 4 5 14 9
6 4 5 15 9
1 4 6 7 9
1 4 6 8 9
5 4 6 7 9
5 4 6 8 9
4 6 8 9 9
4 6 8 10 9
7 6 8 9 9
7 6 8 10 9
6 8 10 11 9
6 8 10 12 9
9 8 10 11 9
9 8 10 12 9
8 10 12 1 9
8 10 12 13 9
11 10 12 1 9
11 10 12 13 9

(sal.pdb)
ATOM 1 C4 SAL S -26.556 -6.032 -1.329 1.00 0.00 SALC
ATOM 2 O1 SAL S -27.438 -6.144 -0.246 1.00 0.00 SALC
ATOM 3 H SAL S -28.284 -5.821 -0.626 1.00 0.00 SALC
ATOM 4 C6 SAL S -27.007 -5.540 -2.555 1.00 0.00 SALC
ATOM 5 C5 SAL S -28.411 -4.989 -2.716 1.00 0.00 SALC
ATOM 6 C0 SAL S -26.094 -5.520 -3.625 1.00 0.00 SALC
ATOM 7 H0 SAL S -26.420 -5.198 -4.597 1.00 0.00 SALC
ATOM 8 C1 SAL S -24.763 -5.894 -3.452 1.00 0.00 SALC
ATOM 9 H1 SAL S -24.083 -5.863 -4.289 1.00 0.00 SALC
ATOM 10 C2 SAL S -24.324 -6.338 -2.212 1.00 0.00 SALC
ATOM 11 H2 SAL S -23.303 -6.653 -2.076 1.00 0.00 SALC
ATOM 12 C3 SAL S -25.232 -6.427 -1.160 1.00 0.00 SALC
ATOM 13 H3 SAL S -24.915 -6.828 -0.211 1.00 0.00 SALC
ATOM 14 O2 SAL S -29.165 -4.988 -1.703 1.00 0.00 SALC
ATOM 15 O0 SAL S -28.745 -4.508 -3.832 1.00 0.00 SALC

How should I go about fixing this issue?

7

Please provide the whole topology. Atom numbers out of context (without knowing what types you’ve assigned) do not mean anything. Likely you have incorrectly chosen an atom type for one of those atoms, such that it does not exist in the force field. These are very simple molecules so there is no reason CGenFF will not support them.

The basis of salicylate should be ZOIC (benzoic acid), not MBOA, if you’re trying to generate the topology yourself. Otherwise just parametrize it with the CGenFF server and let it do everything for you.

As a bit of trivia, MBOA and ZOIC are my contributions to CGenFF, my training project when I joined Alex MacKerell’s group as a postdoc :)

8

Hi Justin, thanks for the quick reply! I have added the whole topology file below. I generated SAL initially using CGenFF, but the penalties were too high. I ended up getting these parameters from the Tajkhorshid lab at UIUC, who optimized them with FFtK. I checked already to ensure that all atom-types were present in atomtypes.atp. I like you bit of trivia, and have now even more confidence than before that you’re the correct person to help with this!! Once again, I highlighted the line that threw the error.

;
; File ‘topol.top’ was generated
; By user: bhaddad (1021)
; On host: ws5
; At date: Wed Nov 10 18:35:33 2021
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.3 (-:
;
; Executable: /usr/local/gromacs-2021.3/bin/gmx
; Data prefix: /usr/local/gromacs-2021.3
; Working dir: /home/bhaddad/ForceFields/Salicylate-Tajkhorshid
; Command line:
; gmx pdb2gmx -f sal.pdb -ignh
; Force field data was read from:
; /home/bhaddad/ForceFields/
;
; Note:
; This might be a non-standard force field location. When you use this topology, the
; force field must either be present in the current directory, or the location
; specified in the GMXLIB path variable or with the ‘include’ mdp file option.
;
[ moleculetype ]
; Name nrexcl
SAL 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 0 SAL rtp SAL q -1.0
1 CG2R61 0 SAL C4 1 0.106 12.011
2 OG311 0 SAL O1 2 -0.532 15.9994
3 HGP1 0 SAL H 3 0.42 1.008
4 CG2R61 0 SAL C6 4 -0.104 12.011
5 CG2O3 0 SAL C5 5 0.624 12.011
6 CG2R61 0 SAL C0 6 -0.116 12.011
7 HGR61 0 SAL H0 7 0.115 1.008
8 CG2R61 0 SAL C1 8 -0.112 12.011
9 HGR61 0 SAL H1 9 0.115 1.008
10 CG2R61 0 SAL C2 10 -0.113 12.011
11 HGR61 0 SAL H2 11 0.115 1.008
12 CG2R61 0 SAL C3 12 -0.113 12.011
13 HGR61 0 SAL H3 13 0.115 1.008
14 OG2D2 0 SAL O2 14 -0.76 15.9994
15 OG2D2 0 SAL O0 15 -0.76 15.9994 ; qtot -1

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 4 1
1 12 1
2 3 1
4 5 1
4 6 1
5 14 1
5 15 1
6 7 1
6 8 1
8 9 1
8 10 1
10 11 1
10 12 1
12 13 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 11 1
1 14 1
1 15 1
2 5 1
2 6 1
2 10 1
2 13 1
3 4 1
3 12 1
4 9 1
4 10 1
4 13 1
5 7 1
5 8 1
5 12 1
6 11 1
6 12 1
6 14 1
6 15 1
7 9 1
7 10 1
8 13 1
9 11 1
9 12 1
11 13 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 4 5
2 1 12 5
4 1 12 5
1 2 3 5
1 4 5 5
1 4 6 5
5 4 6 5
4 5 14 5
4 5 15 5
14 5 15 5
4 6 7 5
4 6 8 5
7 6 8 5
6 8 9 5
6 8 10 5
9 8 10 5
8 10 11 5
8 10 12 5
11 10 12 5
1 12 10 5
1 12 13 5
10 12 13 5

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
4 1 2 3 9
12 1 2 3 9
2 1 4 5 9
2 1 4 6 9
12 1 4 5 9
12 1 4 6 9
2 1 12 10 9
2 1 12 13 9
4 1 12 10 9
4 1 12 13 9
1 4 5 14 9
1 4 5 15 9
6 4 5 14 9
6 4 5 15 9
1 4 6 7 9
1 4 6 8 9
5 4 6 7 9
5 4 6 8 9
4 6 8 9 9
4 6 8 10 9
7 6 8 9 9
7 6 8 10 9
6 8 10 11 9
6 8 10 12 9
9 8 10 11 9
9 8 10 12 9
8 10 12 1 9
8 10 12 13 9
11 10 12 1 9
11 10 12 13 9

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 15 14 4 2

9

There are apparently new dihedral parameters that they derived, so you will need to ask them to provide those parameters. This dihedral should not be challenging to parametrize because it is not a rotatable bond; even some stock parameters by analogy should suffice.

10

Thank you for your help! I was able to fix it by adding the following line to the ffbonded.itp (for future reference).

OG311 CG2R61 CG2R61 CG2O3 9 180.000000 2.400000 2

11

Hi Bhaddad,
Could you figure out the problems:
rated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file unk.itp, line 425]:
No default Proper Dih. types

ERROR 2 [file unk.itp, line 431]:
No default Proper Dih. types

ERROR 3 [file unk.itp, line 443]:
No default Proper Dih. types

ERROR 4 [file unk.itp, line 453]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘UNK’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 72404]:
System has non-zero total charge: -3.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.

itp file
; Created by cgenff_charmm2gmx.py

[ moleculetype ]
; Name nrexcl
UNK 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 UNK rtp UNK q qsum
1 CG2R61 1 UNK C1 1 -0.114 12.011 ;
2 CG2R61 1 UNK C2 2 0.000 12.011 ;
3 CG2R61 1 UNK C3 3 -0.114 12.011 ;
4 CG2R61 1 UNK C4 4 -0.112 12.011 ;
5 CG2R61 1 UNK C5 5 0.222 12.011 ;
6 CG2R61 1 UNK C6 6 -0.112 12.011 ;
7 OG301 1 UNK O1 7 -0.427 15.999 ;
8 CG311 1 UNK C7 8 0.280 12.011 ;
9 OG3C61 1 UNK O2 9 -0.398 15.999 ;
10 CG311 1 UNK C8 10 0.062 12.011 ;
11 CG311 1 UNK C9 11 0.147 12.011 ;
12 CG311 1 UNK C10 12 0.149 12.011 ;
13 CG311 1 UNK C11 13 0.156 12.011 ;
14 OG311 1 UNK O3 14 -0.646 15.999 ;
15 OG311 1 UNK O4 15 -0.642 15.999 ;
16 OG311 1 UNK O5 16 -0.645 15.999 ;
17 CG321 1 UNK C12 17 0.082 12.011 ;
18 OG311 1 UNK O6 18 -0.646 15.999 ;
19 CG321 1 UNK C13 19 -0.188 12.011 ;
20 CG321 1 UNK C14 20 -0.188 12.011 ;
21 CG2R61 1 UNK C15 21 -0.000 12.011 ;
22 CG2R61 1 UNK C16 22 -0.114 12.011 ;
23 CG2R61 1 UNK C17 23 0.224 12.011 ;
24 CG2R61 1 UNK C18 24 -0.115 12.011 ;
25 CG2R61 1 UNK C19 25 0.115 12.011 ;
26 CG2R61 1 UNK C20 26 -0.114 12.011 ;
27 OG311 1 UNK O7 27 -0.531 15.999 ;
28 OG301 1 UNK O8 28 -0.390 15.999 ;
29 CG331 1 UNK C21 29 -0.101 12.011 ;
30 HGR61 1 UNK H1 30 0.115 1.008 ;
31 HGR61 1 UNK H2 31 0.115 1.008 ;
32 HGR61 1 UNK H3 32 0.115 1.008 ;
33 HGR61 1 UNK H4 33 0.115 1.008 ;
34 HGA1 1 UNK H5 34 0.090 1.008 ;
35 HGA1 1 UNK H6 35 0.090 1.008 ;
36 HGA1 1 UNK H7 36 0.090 1.008 ;
37 HGA1 1 UNK H8 37 0.090 1.008 ;
38 HGA1 1 UNK H9 38 0.090 1.008 ;
39 HGP1 1 UNK H10 39 0.419 1.008 ;
40 HGP1 1 UNK H11 40 0.419 1.008 ;
41 HGP1 1 UNK H12 41 0.419 1.008 ;
42 HGA2 1 UNK H13 42 0.090 1.008 ;
43 HGA2 1 UNK H14 43 0.090 1.008 ;
44 HGP1 1 UNK H15 44 0.419 1.008 ;
45 HGA2 1 UNK H16 45 0.090 1.008 ;
46 HGA2 1 UNK H17 46 0.090 1.008 ;
47 HGA2 1 UNK H18 47 0.090 1.008 ;
48 HGA2 1 UNK H19 48 0.090 1.008 ;
49 HGR61 1 UNK H20 49 0.115 1.008 ;
50 HGR61 1 UNK H21 50 0.115 1.008 ;
51 HGR61 1 UNK H22 51 0.115 1.008 ;
52 HGP1 1 UNK H23 52 0.419 1.008 ;
53 HGA3 1 UNK H24 53 0.090 1.008 ;
54 HGA3 1 UNK H25 54 0.090 1.008 ;
55 HGA3 1 UNK H26 55 0.090 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 6 1
1 30 1
2 3 1
2 19 1
3 4 1
3 31 1
4 5 1
4 32 1
5 6 1
5 7 1
6 33 1
7 8 1
8 9 1
8 34 1
8 13 1
9 10 1
10 17 1
10 35 1
10 11 1
11 12 1
11 36 1
11 16 1
12 13 1
12 37 1
12 15 1
13 14 1
13 38 1
14 39 1
15 40 1
16 41 1
17 43 1
17 42 1
17 18 1
18 44 1
19 20 1
19 45 1
19 46 1
20 21 1
20 47 1
20 48 1
21 26 1
21 22 1
22 49 1
22 23 1
23 28 1
23 24 1
24 25 1
24 50 1
25 26 1
25 27 1
26 51 1
27 52 1
28 29 1
29 53 1
29 54 1
29 55 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 20 1
1 7 1
1 45 1
1 46 1
1 31 1
2 33 1
2 21 1
2 5 1
2 48 1
2 47 1
2 32 1
3 20 1
3 6 1
3 7 1
3 45 1
3 46 1
3 30 1
4 33 1
4 19 1
4 8 1
5 34 1
5 9 1
5 13 1
5 30 1
5 31 1
6 8 1
6 19 1
6 32 1
7 33 1
7 38 1
7 10 1
7 12 1
7 14 1
7 32 1
8 17 1
8 35 1
8 37 1
8 39 1
8 11 1
8 15 1
9 18 1
9 36 1
9 38 1
9 42 1
9 43 1
9 12 1
9 14 1
9 16 1
10 34 1
10 37 1
10 41 1
10 44 1
10 13 1
10 15 1
11 18 1
11 38 1
11 42 1
11 43 1
11 40 1
11 14 1
12 17 1
12 34 1
12 35 1
12 39 1
12 41 1
13 36 1
13 40 1
13 16 1
14 34 1
14 37 1
14 15 1
15 36 1
15 38 1
15 16 1
16 17 1
16 35 1
16 37 1
17 36 1
18 35 1
19 26 1
19 30 1
19 31 1
19 22 1
20 49 1
20 23 1
20 25 1
20 51 1
21 24 1
21 27 1
21 28 1
21 45 1
21 46 1
22 50 1
22 25 1
22 29 1
22 51 1
22 47 1
22 48 1
23 53 1
23 54 1
23 55 1
23 26 1
23 27 1
24 49 1
24 29 1
24 51 1
24 52 1
25 28 1
26 49 1
26 50 1
26 52 1
26 47 1
26 48 1
27 50 1
27 51 1
28 49 1
28 50 1
30 33 1
31 32 1
34 38 1
35 36 1
35 42 1
35 43 1
36 41 1
36 37 1
37 38 1
37 40 1
38 39 1
42 44 1
43 44 1
45 47 1
45 48 1
46 47 1
46 48 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 6 5
2 1 30 5
6 1 30 5
1 2 3 5
1 2 19 5
3 2 19 5
2 3 4 5
2 3 31 5
4 3 31 5
3 4 5 5
3 4 32 5
5 4 32 5
4 5 6 5
4 5 7 5
6 5 7 5
1 6 33 5
1 6 5 5
33 6 5 5
5 7 8 5
9 8 34 5
9 8 13 5
9 8 7 5
34 8 13 5
34 8 7 5
13 8 7 5
10 9 8 5
9 10 17 5
9 10 35 5
9 10 11 5
17 10 35 5
17 10 11 5
35 10 11 5
12 11 10 5
12 11 36 5
12 11 16 5
10 11 36 5
10 11 16 5
36 11 16 5
13 12 11 5
13 12 37 5
13 12 15 5
11 12 37 5
11 12 15 5
37 12 15 5
12 13 14 5
12 13 38 5
12 13 8 5
14 13 38 5
14 13 8 5
38 13 8 5
13 14 39 5
12 15 40 5
41 16 11 5
10 17 43 5
10 17 42 5
10 17 18 5
43 17 42 5
43 17 18 5
42 17 18 5
17 18 44 5
2 19 20 5
2 19 45 5
2 19 46 5
20 19 45 5
20 19 46 5
45 19 46 5
19 20 21 5
19 20 47 5
19 20 48 5
21 20 47 5
21 20 48 5
47 20 48 5
26 21 20 5
26 21 22 5
20 21 22 5
49 22 21 5
49 22 23 5
21 22 23 5
28 23 22 5
28 23 24 5
22 23 24 5
25 24 50 5
25 24 23 5
50 24 23 5
26 25 27 5
26 25 24 5
27 25 24 5
25 26 51 5
25 26 21 5
51 26 21 5
25 27 52 5
29 28 23 5
28 29 53 5
28 29 54 5
28 29 55 5
53 29 54 5
53 29 55 5
54 29 55 5

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
6 1 2 3 9
6 1 2 19 9
30 1 2 3 9
30 1 2 19 9
2 1 6 33 9
2 1 6 5 9
30 1 6 33 9
30 1 6 5 9
1 2 3 4 9
1 2 3 31 9
19 2 3 4 9
19 2 3 31 9
1 2 19 20 9
1 2 19 45 9
1 2 19 46 9
3 2 19 20 9
3 2 19 45 9
3 2 19 46 9
2 3 4 5 9
2 3 4 32 9
31 3 4 5 9
31 3 4 32 9
3 4 5 6 9
3 4 5 7 9
32 4 5 6 9
32 4 5 7 9
4 5 6 1 9
4 5 6 33 9
7 5 6 1 9
7 5 6 33 9
4 5 7 8 9
6 5 7 8 9
5 7 8 9 9
5 7 8 34 9
5 7 8 13 9
34 8 9 10 9
13 8 9 10 9
7 8 9 10 9
9 8 13 12 9
9 8 13 14 9
9 8 13 38 9
34 8 13 12 9
34 8 13 14 9
34 8 13 38 9
7 8 13 12 9
7 8 13 14 9
7 8 13 38 9
8 9 10 17 9
8 9 10 35 9
8 9 10 11 9
9 10 17 43 9
9 10 17 42 9
9 10 17 18 9
35 10 17 43 9
35 10 17 42 9
35 10 17 18 9
11 10 17 43 9
11 10 17 42 9
11 10 17 18 9
9 10 11 12 9
9 10 11 36 9
9 10 11 16 9
17 10 11 12 9
17 10 11 36 9
17 10 11 16 9
35 10 11 12 9
35 10 11 36 9
35 10 11 16 9
10 11 12 13 9
10 11 12 37 9
10 11 12 15 9
36 11 12 13 9
36 11 12 37 9
36 11 12 15 9
16 11 12 13 9
16 11 12 37 9
16 11 12 15 9
12 11 16 41 9
10 11 16 41 9
36 11 16 41 9
11 12 13 14 9
11 12 13 38 9
11 12 13 8 9
37 12 13 14 9
37 12 13 38 9
37 12 13 8 9
15 12 13 14 9
15 12 13 38 9
15 12 13 8 9
13 12 15 40 9
11 12 15 40 9
37 12 15 40 9
12 13 14 39 9
38 13 14 39 9
8 13 14 39 9
10 17 18 44 9
43 17 18 44 9
42 17 18 44 9
2 19 20 21 9
2 19 20 47 9
2 19 20 48 9
45 19 20 21 9
45 19 20 47 9
45 19 20 48 9
46 19 20 21 9
46 19 20 47 9
46 19 20 48 9
19 20 21 26 9
19 20 21 22 9
47 20 21 26 9
47 20 21 22 9
48 20 21 26 9
48 20 21 22 9
20 21 26 25 9
20 21 26 51 9
22 21 26 25 9
22 21 26 51 9
26 21 22 49 9
26 21 22 23 9
20 21 22 49 9
20 21 22 23 9
49 22 23 28 9
49 22 23 24 9
21 22 23 28 9
21 22 23 24 9
22 23 28 29 9
24 23 28 29 9
28 23 24 25 9
28 23 24 50 9
22 23 24 25 9
22 23 24 50 9
50 24 25 26 9
50 24 25 27 9
23 24 25 26 9
23 24 25 27 9
27 25 26 51 9
27 25 26 21 9
24 25 26 51 9
24 25 26 21 9
26 25 27 52 9
24 25 27 52 9
23 28 29 53 9
23 28 29 54 9
23 28 29 55 9

12

Hi Santosh,
Did you solve this problem ?
I’m facing same problem . Would you know how can i solve it?