# Error in atomgroup.py: read\_mol2\_coor\_only: no. of atoms in mol2 (37) and top (0) are unequal Usuall

**URL:** <https://gromacs.bioexcel.eu/t/error-in-atomgroup-py-read-mol2-coor-only-no-of-atoms-in-mol2-37-and-top-0-are-unequal-usuall/11664>\
**Category:** User discussions\
**Created:** [March 2, 2025, 12:10pm UTC](https://gromacs.bioexcel.eu/t/error-in-atomgroup-py-read-mol2-coor-only-no-of-atoms-in-mol2-37-and-top-0-are-unequal-usuall/11664 "2025-03-02T12:10:36Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![chen2](https://avatars.discourse-cdn.com/v4/letter/c/b5e925/32.png) [@chen2](https://gromacs.bioexcel.eu/u/chen2)\
**Post date:** [March 2, 2025, 12:10pm UTC](https://gromacs.bioexcel.eu/t/error-in-atomgroup-py-read-mol2-coor-only-no-of-atoms-in-mol2-37-and-top-0-are-unequal-usuall/11664/1 "2025-03-02T12:10:36Z")

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GROMACS version:2022  
GROMACS modification: No  
I encountered some trouble when converting the topology for small molecules. My GROMACS version is 2022. I tried using both the 2022 and 2021 version of the force field files, but neither worked. What could be the issue?  
root@autodl-container-0d98488661-8e306314:~/dock# python cgenff\_charmm2gmx\_py3\_nx2.py SMZ smz\_fix.mol2 smz.str charmm36-jul2021.ff  
NOTE 1: Code tested with Python 3.5.2 and 3.7.3. Your version: 3.8.10 (default, Jun 4 2021, 15:09:15)  
[GCC 7.5.0]

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 smz.str : 4.6  
–Version of CGenFF detected in charmm36-jul2021.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 (37) and top (0) are unequal  
Usually this means the specified residue name does not match between str and mol2 files  
this is my str document

- Toppar stream file generated by
- CHARMM General Force Field (CGenFF) program version 4.0
- For use with CGenFF version 4.6
- 

read rtf card append

- Topologies generated by
- CHARMM General Force Field (CGenFF) program version 4.0
- 

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 \*\*\*\*\* 0.000 ! param penalty= 123.900 ; charge penalty= 47.071  
!RING \* 6 N2 N3 C1 C2 C3 C5  
!RING \* 6 C7 C8 C9 C10 C11 C12  
GROUP ! CHARGE CH\_PENALTY Z EL NB NBE RNG1 TYP RNG2 TYP RNG3 TYP  
ATOM N1 NG311 -0.517 ! 13.866 7 N 3 3  
ATOM N2 NG311 -0.690 ! 37.633 7 N 3 3 6 4  
ATOM N3 NG311 -0.670 ! 16.585 7 N 3 3 6 4  
ATOM N4 NG2S3 -0.824 ! 0.000 7 N 3 3  
ATOM C1 CG311 0.581 ! 23.161 6 C 4 4 6 4  
ATOM C2 CG2D1O 0.037 ! 47.071 6 C 3 4 6 4  
ATOM C3 CG2D1 -0.264 ! 26.532 6 C 3 4 6 4  
ATOM C4 CG331 -0.196 ! 36.247 6 C 4 4  
ATOM C5 CG311 0.142 ! 15.870 6 C 4 4 6 4  
ATOM C6 CG331 -0.265 ! 5.529 6 C 4 4  
ATOM C7 CG2R61 0.241 ! 0.304 6 C 3 4 6 1  
ATOM C8 CG2R61 -0.121 ! 0.000 6 C 3 4 6 1  
ATOM C9 CG2R61 -0.098 ! 0.000 6 C 3 4 6 1  
ATOM C10 CG2R61 0.090 ! 0.000 6 C 3 4 6 1  
ATOM C11 CG2R61 -0.098 ! 0.000 6 C 3 4 6 1  
ATOM C12 CG2R61 -0.121 ! 0.000 6 C 3 4 6 1  
ATOM O1 OG2P1 -0.393 ! 0.256 8 O 1 2  
ATOM O2 OG2P1 -0.393 ! 0.256 8 O 1 2  
ATOM S SG3O2 0.357 ! 3.959 16 S 4 6  
ATOM H1 HGP1 0.395 ! 4.543 1 H 1 1  
ATOM H2 HGP4 0.353 ! 0.000 1 H 1 1  
ATOM H3 HGP4 0.353 ! 0.000 1 H 1 1  
ATOM HN1 HGPAM1 0.404 ! 4.927 1 H 1 1  
ATOM HN2 HGPAM1 0.362 ! 6.361 1 H 1 1  
ATOM H4 HGA1 0.090 ! 1.528 1 H 1 1  
ATOM H5 HGA4 0.155 ! 1.530 1 H 1 1  
ATOM H6 HGA3 0.090 ! 2.915 1 H 1 1  
ATOM H7 HGA3 0.090 ! 2.915 1 H 1 1  
ATOM H8 HGA3 0.090 ! 2.915 1 H 1 1  
ATOM H9 HGA1 0.090 ! 0.507 1 H 1 1  
ATOM H10 HGA3 0.090 ! 0.306 1 H 1 1  
ATOM H11 HGA3 0.090 ! 0.306 1 H 1 1  
ATOM H12 HGA3 0.090 ! 0.306 1 H 1 1  
ATOM H13 HGR61 0.115 ! 0.000 1 H 1 1  
ATOM H14 HGR61 0.115 ! 0.000 1 H 1 1  
ATOM H15 HGR61 0.115 ! 0.000 1 H 1 1  
ATOM H16 HGR61 0.115 ! 0.000 1 H 1 1  
! TYP INR  
BOND N1 S ! 1 0  
BOND N1 C1 ! 1 0  
BOND N1 H1 ! 1 0  
BOND N2 C2 ! 1 1  
BOND N2 C1 ! 1 1  
BOND N2 HN1 ! 1 0  
BOND N3 C5 ! 1 1  
BOND N3 HN2 ! 1 0  
BOND N3 C1 ! 1 1  
BOND N4 H3 ! 1 0  
BOND N4 C10 ! 1 0  
BOND N4 H2 ! 1 0  
BOND C1 H4 ! 1 0  
BOND C2 C3 ! 2 1  
BOND C2 C4 ! 1 0  
BOND C3 C5 ! 1 1  
BOND C3 H5 ! 1 0  
BOND C4 H6 ! 1 0  
BOND C4 H7 ! 1 0  
BOND C4 H8 ! 1 0  
BOND C5 C6 ! 1 0  
BOND C5 H9 ! 1 0  
BOND C6 H10 ! 1 0  
BOND C6 H11 ! 1 0  
BOND C6 H12 ! 1 0  
BOND C7 S ! 1 0  
BOND C7 C12 ! 2 1  
BOND C7 C8 ! 1 1  
BOND C8 C9 ! 2 1  
BOND C8 H13 ! 1 0  
BOND C9 C10 ! 1 1  
BOND C9 H14 ! 1 0  
BOND C10 C11 ! 2 1  
BOND C11 C12 ! 1 1  
BOND C11 H15 ! 1 0  
BOND C12 H16 ! 1 0  
BOND O1 S ! 2 0  
BOND O2 S ! 2 0  
IMPR N4 H2 H3 C10  
IMPR C2 C3 C4 N2

END

read param card flex append

- Parameters generated by analogy by
- CHARMM General Force Field (CGenFF) program version 4.0
- 

! 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  
CG311 NG311 263.00 1.4740 ! \*\*\*\*\* , from CG314 NG311, penalty= 1

ANGLES  
CG2D1O CG2D1 CG311 40.00 127.50 ! \*\*\*\*\* , from CG2D2O CG2D1 CG321, penalty= 0.6  
CG2D1 CG2D1O CG331 48.00 123.50 ! \*\*\*\*\* , from CG2D1 CG2D1 CG331, penalty= 30  
CG331 CG2D1O NG311 48.00 123.50 ! \*\*\*\*\* , from CG321 CG2D1 CG331, penalty= 69  
CG2D1 CG311 CG331 32.00 112.20 ! \*\*\*\*\* , from CG2D1 CG311 CG321, penalty= 0.9  
CG2D1 CG311 NG311 78.00 110.00 ! \*\*\*\*\* , from CG2D1 CG321 NG311, penalty= 4  
CG331 CG311 NG311 73.00 113.20 ! \*\*\*\*\* , from CG331 CG311 NG321, penalty= 1.2  
NG311 CG311 NG311 90.00 113.00 ! \*\*\*\*\* , from NG311 CG321 NG311, penalty= 4  
NG311 CG311 HGA1 32.40 109.50 50.00 2.13000 ! \*\*\*\*\* , from NG311 CG314 HGA1, penalty= 1  
CG2D1O NG311 CG311 70.00 121.70 ! \*\*\*\*\* , from CG2D2O NG301 CG3C51, penalty= 16.4  
CG311 NG311 CG311 40.50 109.60 ! \*\*\*\*\* , from CG321 NG311 CG321, penalty= 1.2  
CG311 NG311 SG3O2 60.00 115.00 ! \*\*\*\*\* , from CG321 NG311 SG3O2, penalty= 0.6  
CG311 NG311 HGP1 46.00 111.00 ! \*\*\*\*\* , from CG321 NG311 HGP1, penalty= 0.6  
CG311 NG311 HGPAM1 35.00 111.00 ! \*\*\*\*\* , from CG321 NG311 HGPAM1, penalty= 0.6

DIHEDRALS  
CG311 CG2D1 CG2D1O CG331 0.4500 1 180.00 ! \*\*\*\*\* , from CG321 CG2D1 CG2D1 CG331, penalty= 30.6  
CG311 CG2D1 CG2D1O CG331 8.5000 2 180.00 ! \*\*\*\*\* , from CG321 CG2D1 CG2D1 CG331, penalty= 30.6  
CG311 CG2D1 CG2D1O NG311 3.0000 2 180.00 ! \*\*\*\*\* , from CG321 CG2D1 CG2D2O NG311, penalty= 0.6  
HGA4 CG2D1 CG2D1O CG331 1.0000 2 180.00 ! \*\*\*\*\* , from CG331 CG2D1 CG2D1 HGA4, penalty= 30  
CG2D1O CG2D1 CG311 CG331 0.6000 1 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1 CG311 CG321, penalty= 3.9  
CG2D1O CG2D1 CG311 NG311 1.6000 1 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1 CG321 NG311, penalty= 7  
CG2D1O CG2D1 CG311 NG311 0.3000 3 0.00 ! \*\*\*\*\* , from CG2D1 CG2D1 CG321 NG311, penalty= 7  
CG2D1O CG2D1 CG311 HGA1 0.3000 3 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1 CG311 HGA1, penalty= 3  
HGA4 CG2D1 CG311 CG331 0.1200 3 0.00 ! \*\*\*\*\* , from HGA4 CG2D1 CG311 CG321, penalty= 0.9  
HGA4 CG2D1 CG311 NG311 0.2600 3 0.00 ! \*\*\*\*\* , from HGA4 CG2D1 CG321 NG311, penalty= 4  
CG2D1 CG2D1O CG331 HGA3 0.3000 3 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1 CG331 HGA3, penalty= 30  
NG311 CG2D1O CG331 HGA3 0.1600 3 0.00 ! \*\*\*\*\* , from CG321 CG2D1 CG331 HGA3, penalty= 69  
CG2D1 CG2D1O NG311 CG311 0.1000 2 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1O NG301 CG3C51, penalty= 16.4  
CG331 CG2D1O NG311 CG311 0.1000 2 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1O NG301 CG3C51, penalty= 123.9  
CG331 CG2D1O NG311 HGPAM1 0.1000 2 180.00 ! \*\*\*\*\* , from CG2D1 CG2D1O NG311 HGPAM1, penalty= 107.5  
CG2D1 CG311 CG331 HGA3 0.1600 3 0.00 ! \*\*\*\*\* , from CG2D1 CG321 CG331 HGA3, penalty= 4  
NG311 CG311 CG331 HGA3 0.1600 3 0.00 ! \*\*\*\*\* , from NG321 CG311 CG331 HGA3, penalty= 1.2  
CG2D1 CG311 NG311 CG311 1.1000 1 180.00 ! \*\*\*\*\* , from CG2D1 CG321 NG311 CG321, penalty= 4.6  
CG2D1 CG311 NG311 CG311 0.6000 2 180.00 ! \*\*\*\*\* , from CG2D1 CG321 NG311 CG321, penalty= 4.6  
CG2D1 CG311 NG311 CG311 0.5000 3 0.00 ! \*\*\*\*\* , from CG2D1 CG321 NG311 CG321, penalty= 4.6  
CG2D1 CG311 NG311 HGPAM1 0.4800 3 0.00 ! \*\*\*\*\* , from CG2D1 CG321 NG311 HGPAM1, penalty= 4  
CG331 CG311 NG311 CG311 1.4200 1 180.00 ! \*\*\*\*\* , from CG321 CG321 NG301 CG321, penalty= 10.5  
CG331 CG311 NG311 CG311 0.8200 2 0.00 ! \*\*\*\*\* , from CG321 CG321 NG301 CG321, penalty= 10.5  
CG331 CG311 NG311 CG311 1.0200 3 0.00 ! \*\*\*\*\* , from CG321 CG321 NG301 CG321, penalty= 10.5  
CG331 CG311 NG311 HGPAM1 0.3000 3 0.00 ! \*\*\*\*\* , from CG321 CG321 NG311 HGPAM1, penalty= 4.9  
NG311 CG311 NG311 CG2D1O 2.5000 1 180.00 ! \*\*\*\*\* , from NG311 CG321 NG311 CG2R61, penalty= 25  
NG311 CG311 NG311 CG2D1O 1.5000 2 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 CG2R61, penalty= 25  
NG311 CG311 NG311 CG2D1O 0.5000 3 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 CG2R61, penalty= 25  
NG311 CG311 NG311 CG311 0.4115 1 0.00 ! \*\*\*\*\* , from NG3P3 CG314 NG311 CG321, penalty= 38.5  
NG311 CG311 NG311 CG311 0.4772 2 0.00 ! \*\*\*\*\* , from NG3P3 CG314 NG311 CG321, penalty= 38.5  
NG311 CG311 NG311 CG311 0.5266 3 0.00 ! \*\*\*\*\* , from NG3P3 CG314 NG311 CG321, penalty= 38.5  
NG311 CG311 NG311 SG3O2 1.4000 1 180.00 ! \*\*\*\*\* , from NG311 CG321 NG311 SG3O2, penalty= 4  
NG311 CG311 NG311 SG3O2 0.5000 2 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 SG3O2, penalty= 4  
NG311 CG311 NG311 SG3O2 0.1000 3 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 SG3O2, penalty= 4  
NG311 CG311 NG311 HGP1 0.1000 3 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 HGP1, penalty= 4  
NG311 CG311 NG311 HGPAM1 1.7000 2 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 HGPAM1, penalty= 4  
NG311 CG311 NG311 HGPAM1 0.3000 3 0.00 ! \*\*\*\*\* , from NG311 CG321 NG311 HGPAM1, penalty= 4  
HGA1 CG311 NG311 CG2D1O 0.0000 3 180.00 ! \*\*\*\*\* , from HGA2 CG321 NG311 CG2R61, penalty= 25  
HGA1 CG311 NG311 CG311 0.0000 3 0.00 ! \*\*\*\*\* , from HGA1 CG314 NG311 CG321, penalty= 1.6  
HGA1 CG311 NG311 SG3O2 0.1000 3 0.00 ! \*\*\*\*\* , from HGA2 CG321 NG311 SG3O2, penalty= 4  
HGA1 CG311 NG311 HGP1 0.0500 3 0.00 ! \*\*\*\*\* , from HGA1 CG314 NG311 HGPAM1, penalty= 2  
HGA1 CG311 NG311 HGPAM1 0.0500 3 0.00 ! \*\*\*\*\* , from HGA1 CG314 NG311 HGPAM1, penalty= 1  
CG311 NG311 SG3O2 CG2R61 1.5000 2 0.00 ! \*\*\*\*\* , from CG321 NG311 SG3O2 CG2R61, penalty= 0.6  
CG311 NG311 SG3O2 CG2R61 0.5000 3 0.00 ! \*\*\*\*\* , from CG321 NG311 SG3O2 CG2R61, penalty= 0.6  
CG311 NG311 SG3O2 OG2P1 0.2000 3 0.00 ! \*\*\*\*\* , from CG321 NG311 SG3O2 OG2P1, penalty= 0.6

IMPROPERS  
CG2D1O CG2D1 CG331 NG311 53.0000 0 0.00 ! \*\*\*\*\* , from CG2D1O CG2D1 NG311 HGA4, penalty= 81.8

END  
RETURN