Can anyone please help me

User discussions
1

NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.7.17 (default, Jun 6 2023, 20:10:09)
[GCC 11.3.0]

NOTE 2: Code tested with NetworkX 2.3. Your version: 2.3

NOTE 3: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in lig.str : 4.6
–Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6

NOTE 4: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF.
Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (46) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files

lig.str file

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 2.5
  • For use with CGenFF version 4.6

read rtf card append

  • Topologies generated by
  • CHARMM General Force Field (CGenFF) program version 2.5

36 1

! “penalty” is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI lig 0.000 ! param penalty= 416.000 ; charge penalty= 334.943
GROUP ! CHARGE CH_PENALTY
ATOM N1 NG2D1 -0.358 ! 334.943
ATOM N2 NG2D1 -0.358 ! 334.943
ATOM C1 CG2R61 0.244 ! 2.500
ATOM C2 CG2R61 0.244 ! 2.500
ATOM C3 CG2R61 0.226 ! 0.750
ATOM C4 CG2R61 0.226 ! 0.750
ATOM C5 CG2R61 0.226 ! 0.750
ATOM C6 CG2R61 0.226 ! 0.750
ATOM C7 CG2R61 0.111 ! 1.061
ATOM C8 CG2R61 0.111 ! 1.061
ATOM C9 CG2R61 -0.116 ! 0.000
ATOM C10 CG2R61 -0.116 ! 0.000
ATOM C11 CG2R61 -0.116 ! 0.000
ATOM C12 CG2R61 -0.116 ! 0.000
ATOM C13 CG2DC1 -0.077 ! 270.265
ATOM C14 CG2DC1 -0.077 ! 270.265
ATOM C15 CG331 -0.101 ! 0.000
ATOM C16 CG331 -0.101 ! 0.000
ATOM C17 CG331 -0.101 ! 0.000
ATOM C18 CG331 -0.101 ! 0.000
ATOM O1 OG301 -0.389 ! 0.750
ATOM O2 OG301 -0.389 ! 0.750
ATOM O3 OG301 -0.389 ! 0.750
ATOM O4 OG301 -0.389 ! 0.750
ATOM O5 OG311 -0.543 ! 1.061
ATOM O6 OG311 -0.543 ! 1.061
ATOM H1 HGR61 0.115 ! 0.000
ATOM H2 HGR61 0.115 ! 0.000
ATOM H3 HGR61 0.115 ! 0.000
ATOM H4 HGR61 0.115 ! 0.000
ATOM H5 HGA4 0.193 ! 2.500
ATOM H6 HGA4 0.193 ! 2.500
ATOM H7 HGP1 0.420 ! 0.000
ATOM H8 HGP1 0.420 ! 0.000
ATOM H9 HGA3 0.090 ! 0.000
ATOM H10 HGA3 0.090 ! 0.000
ATOM H11 HGA3 0.090 ! 0.000
ATOM H12 HGA3 0.090 ! 0.000
ATOM H13 HGA3 0.090 ! 0.000
ATOM H14 HGA3 0.090 ! 0.000
ATOM H15 HGA3 0.090 ! 0.000
ATOM H16 HGA3 0.090 ! 0.000
ATOM H17 HGA3 0.090 ! 0.000
ATOM H18 HGA3 0.090 ! 0.000
ATOM H19 HGA3 0.090 ! 0.000
ATOM H20 HGA3 0.090 ! 0.000

BOND N1 N2
BOND N1 C13
BOND N2 C14
BOND C1 C9
BOND C1 C11
BOND C1 C13
BOND C2 C10
BOND C2 C12
BOND C2 C14
BOND C3 C7
BOND C3 C9
BOND C3 O1
BOND C4 C8
BOND C4 C10
BOND C4 O2
BOND C5 C7
BOND C5 C11
BOND C5 O3
BOND C6 C8
BOND C6 C12
BOND C6 O4
BOND C7 O5
BOND C8 O6
BOND C9 H1
BOND C10 H2
BOND C11 H3
BOND C12 H4
BOND C13 H5
BOND C14 H6
BOND C15 O1
BOND C15 H9
BOND C15 H10
BOND C15 H11
BOND C16 O2
BOND C16 H12
BOND C16 H13
BOND C16 H14
BOND C17 O3
BOND C17 H15
BOND C17 H16
BOND C17 H17
BOND C18 O4
BOND C18 H18
BOND C18 H19
BOND C18 H20
BOND O5 H7
BOND O6 H8
IMPR C13 C1 N1 H5
IMPR C14 C2 N2 H6

END

read param card flex append

  • Parameters generated by analogy by
  • CHARMM General Force Field (CGenFF) program version 2.5

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS

ANGLES
CG2DC1 NG2D1 NG2D1 100.00 115.00 ! lig , from CG2DC1 NG2D1 NG2S1, penalty= 416

DIHEDRALS
CG2R61 CG2DC1 NG2D1 NG2D1 12.0000 2 180.00 ! lig , from CG2R61 CG2DC1 NG2D1 NG2S1, penalty= 56
HGA4 CG2DC1 NG2D1 NG2D1 4.0000 2 180.00 ! lig , from HGA4 CG2DC1 NG2D1 NG2S1, penalty= 56
OG301 CG2R61 CG2R61 OG311 3.3808 2 180.00 ! lig , from OG311 CG2R61 CG2R61 OG311, penalty= 15
CG2DC1 NG2D1 NG2D1 CG2DC1 15.2000 2 180.00 ! lig , from CG2R61 NG2D1 NG2D1 CG2R61, penalty= 122
CG2DC1 NG2D1 NG2D1 CG2DC1 0.5000 4 0.00 ! lig , from CG2R61 NG2D1 NG2D1 CG2R61, penalty= 122

IMPROPERS

END
RETURN

lig_fix.mol2
@MOLECULE
lig
46 47 1
SMALL
USER_CHARGES
@ATOM
1 N -0.635 -0.286 0.001 N.2 1 UNK0 0.000
2 N 0.633 0.284 0.001 N.2 1 UNK0 0.000
3 C -2.983 0.309 0.001 C.2 1 UNK0 0.000
4 C 2.982 -0.310 0.001 C.2 1 UNK0 0.000
5 C -4.759 -1.329 -0.001 C.2 1 UNK0 0.000
6 C 4.757 1.329 -0.001 C.2 1 UNK0 0.000
7 C -5.289 1.028 -0.000 C.2 1 UNK0 0.000
8 C 5.288 -1.028 -0.000 C.2 1 UNK0 0.000
9 C -5.705 -0.303 -0.001 C.2 1 UNK0 0.000
10 C 5.703 0.304 -0.001 C.2 1 UNK0 0.000
11 C -3.398 -1.023 -0.000 C.2 1 UNK0 0.000
12 C 3.396 1.022 -0.000 C.2 1 UNK0 0.000
13 C -3.928 1.334 0.001 C.2 1 UNK0 0.000
14 C 3.928 -1.335 0.001 C.2 1 UNK0 0.000
15 C -1.546 0.632 0.001 C.2 1 UNK0 0.000
16 C 1.563 -0.629 0.002 C.2 1 UNK0 0.000
17 C -4.121 -3.620 -0.001 C.3 1 UNK0 0.000
18 C 4.117 3.619 -0.001 C.3 1 UNK0 0.000
19 C -5.694 3.372 0.002 C.3 1 UNK0 0.000
20 C 5.694 -3.371 0.002 C.3 1 UNK0 0.000
21 O -5.151 -2.634 -0.001 O.3 1 UNK0 0.000
22 O 5.148 2.634 -0.001 O.3 1 UNK0 0.000
23 O -6.203 2.039 0.001 O.3 1 UNK0 0.000
24 O 6.202 -2.038 0.001 O.3 1 UNK0 0.000
25 O -7.035 -0.603 -0.004 O.3 1 UNK0 0.000
26 O 7.033 0.604 -0.004 O.3 1 UNK0 0.000
27 H -2.630 -1.788 -0.000 H 1 UNK0 0.000
28 H 2.628 1.787 -0.000 H 1 UNK0 0.000
29 H -3.548 2.350 0.002 H 1 UNK0 0.000
30 H 3.549 -2.351 0.002 H 1 UNK0 0.000
31 H -1.278 1.705 0.002 H 1 UNK0 0.000
32 H 1.289 -1.701 0.002 H 1 UNK0 0.000
33 H -7.131 -1.571 -0.005 H 1 UNK0 0.000
34 H 7.536 -0.230 -0.004 H 1 UNK0 0.000
35 H -3.514 -3.571 -0.912 H 1 UNK0 0.000
36 H -3.514 -3.571 0.910 H 1 UNK0 0.000
37 H -4.613 -4.598 -0.001 H 1 UNK0 0.000
38 H 3.511 3.570 -0.912 H 1 UNK0 0.000
39 H 3.511 3.571 0.910 H 1 UNK0 0.000
40 H 4.609 4.598 -0.001 H 1 UNK0 0.000
41 H -5.124 3.587 -0.908 H 1 UNK0 0.000
42 H -5.125 3.586 0.913 H 1 UNK0 0.000
43 H -6.557 4.045 0.002 H 1 UNK0 0.000
44 H 5.125 -3.586 0.913 H 1 UNK0 0.000
45 H 5.125 -3.587 -0.908 H 1 UNK0 0.000
46 H 6.558 -4.044 0.002 H 1 UNK0 0.000
@BOND
1 1 2 1
2 1 15 2
3 2 16 2
4 3 11 ar
5 3 13 ar
6 3 15 1
7 4 12 ar
8 4 14 ar
9 4 16 1
10 5 9 ar
11 5 11 ar
12 5 21 1
13 6 10 ar
14 6 12 ar
15 6 22 1
16 7 9 ar
17 7 13 ar
18 7 23 1
19 8 10 ar
20 8 14 ar
21 8 24 1
22 9 25 1
23 10 26 1
24 11 27 1
25 12 28 1
26 13 29 1
27 14 30 1
28 15 31 1
29 16 32 1
30 17 21 1
31 17 35 1
32 17 36 1
33 17 37 1
34 18 22 1
35 18 38 1
36 18 39 1
37 18 40 1
38 19 23 1
39 19 41 1
40 19 42 1
41 19 43 1
42 20 24 1
43 20 44 1
44 20 45 1
45 20 46 1
46 25 33 1
47 26 34 1

2

Dear Ashutosh,

Can you please provide some more information about what you’re trying to do and the problem you are experiencing?

3

now i am encountering new problem i started it again from starting i am doing work on metalloprotein laccase which contain 4 copper ion and now in equlibration ligand name is not coming

gmx make_ndx -f ligand.gro -o index_ligand.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 1 Protein residues
Analysing Protein…

0 System : 25 atoms
1 Protein : 25 atoms
2 Protein-H : 13 atoms
3 C-alpha : 0 atoms
4 Backbone : 0 atoms
5 MainChain : 1 atoms
6 MainChain+Cb : 1 atoms
7 MainChain+H : 4 atoms
8 SideChain : 21 atoms
9 SideChain-H : 12 atoms

as here i selected system but in next to next step where ligand is required to make protein_ligand here problem comes where ligand is not showing

gmx make_ndx -f em.gro -o index.ndx

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are: 526 Protein residues
There are: 4 Other residues
There are: 67740 Water residues
There are: 36 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…

0 System : 211498 atoms
1 Protein : 8238 atoms
2 Protein-H : 4221 atoms
3 C-alpha : 525 atoms
4 Backbone : 1575 atoms
5 MainChain : 2100 atoms
6 MainChain+Cb : 2587 atoms
7 MainChain+H : 2595 atoms
8 SideChain : 5643 atoms
9 SideChain-H : 2121 atoms
10 Prot-Masses : 8238 atoms
11 non-Protein : 203260 atoms
12 Other : 4 atoms
13 CUM : 4 atoms
14 NA : 36 atoms
15 Water : 203220 atoms
16 SOL : 203220 atoms
17 non-Water : 8278 atoms
18 Ion : 36 atoms
19 CUM : 4 atoms
20 NA : 36 atoms
21 Water_and_ions : 203256 atoms

4

We require precise details and unfortunately copy/pasting the error is not sufficient. Please specify which step is generating this error. thank you

5

now can it help its in Restraining the Ligand just above your comment i have updated the problem i am facing

6

and here is the topol file

;
; File ‘topol.top’ was generated
; By user: unknown (1000)
; On host: GodofWar
; At date: Tue Oct 31 19:06:49 2023
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-:
;
; Executable: /usr/bin/gmx
; Data prefix: /usr
; Working dir: /mnt/c/Users/Dell/OneDrive/Desktop/2+ cu serotonin
; Command line:
; gmx pdb2gmx -f protein.pdb -o protein_processed.gro -ter -ignh
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include “./charmm36-jul2022.ff/forcefield.itp”

; Include ligand parameters
#include “ser.prm”

; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Other_chain_B.itp”

; Include water topology
#include “./charmm36-jul2022.ff/tip3p.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “./charmm36-jul2022.ff/ions.itp”

; Include ligand topology
#include “ser.itp”

#ifdef POSRES
#include “posre_ser.itp”
#endif

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
Other_chain_B 1
ser 1
SOL 67740
NA 36

7

As I replied before, please look at the GROMACS tutorials for more details: Introduction to molecular dynamics, tool documentation, or run gmx make_ndx -h in the terminal to get more information. Alternatively create a desired group manually in the index file (usually as index.ndx).