# Can anyone please help me **URL:** \ **Category:** User discussions\ **Tags:** forcefield\ **Created:** [October 22, 2023, 11:22am UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451 "2023-10-22T11:22:57Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [October 22, 2023, 11:22am UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/1 "2023-10-22T11:22:58Z")
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 ---
**Author:** ![cathrine](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cathrine/32/1736_2.png) [@cathrine](https://gromacs.bioexcel.eu/u/cathrine)\ **Post date:** [October 30, 2023, 4:27pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/2 "2023-10-30T16:27:48Z")
Dear Ashutosh, Can you please provide some more information about what you’re trying to do and the problem you are experiencing? ---
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [October 30, 2023, 5:33pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/3 "2023-10-30T17:33:04Z")
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 ---
**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\ **Post date:** [October 31, 2023, 2:37pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/4 "2023-10-31T14:37:43Z")
We require precise details and unfortunately copy/pasting the error is not sufficient. Please specify which step is generating this error. thank you ---
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [October 31, 2023, 2:43pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/5 "2023-10-31T14:43:19Z")
now can it help its in Restraining the Ligand just above your comment i have updated the problem i am facing ---
**Author:** ![Ashutosh](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ashutosh/32/2587_2.png) [@Ashutosh](https://gromacs.bioexcel.eu/u/Ashutosh)\ **Post date:** [October 31, 2023, 2:49pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/6 "2023-10-31T14:49:45Z")
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 ---
**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\ **Post date:** [October 31, 2023, 3:38pm UTC](https://gromacs.bioexcel.eu/t/can-anyone-please-help-me/7451/7 "2023-10-31T15:38:04Z")
As I replied before, please look at the GROMACS tutorials for more details: [Introduction to molecular dynamics](https://tutorials.gromacs.org/md-intro-tutorial.html), [tool documentation](https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html), 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).