CGenff Error: specified residue name does not match between str and mol2 files

Hello,

I try to use CGenff for Gromacs to gernerate topologies for CHARMM36. I took a pdb file from the Automated Topology Builder. Then I gave it to the Discovery Studio Visualizer to get my mol2, which I uploaded at ParamChem to get my str. I can’t generate a output because of an error I posted below.
I’m a newbie and I really can’t find the problem. Sorry for the long post, but I would appreciate help so much.

python2 ./cgenff_charmm2gmx.py TETRAMATHYLP tetramathylp.mol2 tetramathylp.str charmm36-jun2015.ff/

NOTE1: Code tested with python 2.7.3. Your version: 2.7.18 (default, Aug 4 2020, 11:16:42)
[GCC 9.3.0]
NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:
–Version of CGenFF detected in tetramathylp.str : 3.0.1
–Version of CGenFF detected in charmm36-jun2015.ff//forcefield.doc : 3.0.1
NOTE3: In order 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 (22) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files

This is my str:

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 1.0.0
  • For use with CGenFF version 3.0.1

read rtf card append

  • Topologies generated by
  • CHARMM General Force Field (CGenFF) program version 1.0.0

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 All-At 0.000 ! param penalty= 0.000 ; charge penalty= 21.163
GROUP ! CHARGE CH_PENALTY
ATOM H12 HGA3 0.090 ! 2.250
ATOM C8 CG331 -0.270 ! 14.965
ATOM H10 HGA3 0.090 ! 2.250
ATOM H11 HGA3 0.090 ! 2.250
ATOM C7 CG2R61 0.293 ! 16.817
ATOM C2 CG2R61 0.293 ! 16.817
ATOM C1 CG331 -0.270 ! 14.965
ATOM H1 HGA3 0.090 ! 2.250
ATOM H2 HGA3 0.090 ! 2.250
ATOM H3 HGA3 0.090 ! 2.250
ATOM N1 NG2R60 -0.586 ! 21.163
ATOM C3 CG2R61 0.293 ! 16.817
ATOM C4 CG331 -0.270 ! 14.965
ATOM H4 HGA3 0.090 ! 2.250
ATOM H5 HGA3 0.090 ! 2.250
ATOM H6 HGA3 0.090 ! 2.250
ATOM C5 CG2R61 0.293 ! 16.817
ATOM N2 NG2R60 -0.586 ! 21.163
ATOM C6 CG331 -0.270 ! 14.965
ATOM H7 HGA3 0.090 ! 2.250
ATOM H8 HGA3 0.090 ! 2.250
ATOM H9 HGA3 0.090 ! 2.250

BOND H12 C8
BOND C8 H10
BOND C8 H11
BOND C8 C7
BOND C7 C2
BOND C7 N2
BOND C2 C1
BOND C2 N1
BOND C1 H1
BOND C1 H2
BOND C1 H3
BOND N1 C3
BOND C3 C4
BOND C3 C5
BOND C4 H4
BOND C4 H5
BOND C4 H6
BOND C5 N2
BOND C5 C6
BOND C6 H7
BOND C6 H8
BOND C6 H9

END

read param card flex append

  • Parameters generated by analogy by
  • CHARMM General Force Field (CGenFF) program version 1.0.0

! 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

ANGLES

DIHEDRALS

IMPROPERS

This is the mol2:

Created by: Discovery Studio

Creation time: 2020-11-23T14:27:44Z

@MOLECULE
All-Atom(original geometry)_tetramathylp
22 22 1 0 0
PROTEIN
USER_CHARGES

@ATOM
1 H12 -2.956000 -1.609000 0.439000 H 1 WIC0 0.0296
2 C8 -2.432000 -0.951000 1.140000 C.3 1 WIC0 -0.0204
3 H10 -3.084000 -0.116000 1.412000 H 1 WIC0 0.0296
4 H11 -2.227000 -1.526000 2.049000 H 1 WIC0 0.0296
5 C7 -1.160000 -0.446000 0.531000 C.ar 1 WIC0 0.0588
6 C2 -1.149000 0.317000 -0.638000 C.ar 1 WIC0 0.0588
7 C1 -2.408000 0.682000 -1.362000 C.3 1 WIC0 -0.0204
8 H1 -2.185000 1.280000 -2.252000 H 1 WIC0 0.0296
9 H2 -3.064000 1.273000 -0.716000 H 1 WIC0 0.0296
10 H3 -2.936000 -0.220000 -1.689000 H 1 WIC0 0.0296
11 N1 0.011000 0.769000 -1.178000 N.ar 1 WIC0 -0.2546
12 C3 1.160000 0.446000 -0.531000 C.ar 1 WIC0 0.0588
13 C4 2.432000 0.951000 -1.140000 C.3 1 WIC0 -0.0204
14 H4 2.956000 1.609000 -0.439000 H 1 WIC0 0.0296
15 H5 2.227000 1.526000 -2.049000 H 1 WIC0 0.0296
16 H6 3.084000 0.116000 -1.412000 H 1 WIC0 0.0296
17 C5 1.149000 -0.317000 0.638000 C.ar 1 WIC0 0.0588
18 N2 -0.011000 -0.769000 1.178000 N.ar 1 WIC0 -0.2546
19 C6 2.408000 -0.682000 1.362000 C.3 1 WIC0 -0.0204
20 H7 2.936000 0.220000 1.690000 H 1 WIC0 0.0296
21 H8 2.185000 -1.280000 2.252000 H 1 WIC0 0.0296
22 H9 3.064000 -1.273000 0.716000 H 1 WIC0 0.0296
@BOND
1 1 2 1
2 2 3 1
3 2 4 1
4 2 5 1
5 5 6 ar
6 5 18 ar
7 6 7 1
8 6 11 ar
9 7 8 1
10 7 9 1
11 7 10 1
12 11 12 ar
13 12 13 1
14 12 17 ar
15 13 14 1
16 13 15 1
17 13 16 1
18 17 18 ar
19 17 19 1
20 19 20 1
21 19 21 1
22 19 22 1
@SUBSTRUCTURE
1 WIC0 1 RESIDUE 1 _ WIC
@SET
GROUP:Hetatm STATIC ATOMS
22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
@MOL_PROPERTY
PDBRemarks
SciTegic.value.StringValue
HEADER UNCLASSIFIED 09-Jul-20
TITLE ALL ATOM STRUCTURE FOR MOLECULE UNL
AUTHOR GROMOS AUTOMATIC TOPOLOGY BUILDER REVISION 2020-06-20 22:00:16
AUTHOR 2 http://compbio.biosci.uq.edu.au/atb

@MOL_PROPERTY
PDBSeqres
SciTegic.value.StringValue

@ATOM_PROPERTY
Formal Charge
SciTegic.value.StringValue
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
21 0
22 0

@ATOM_PROPERTY
pdb_tempFactor
SciTegic.value.DoubleValue
1 0.00
2 0.00
3 0.00
4 0.00
5 0.00
6 0.00
7 0.00
8 0.00
9 0.00
10 0.00
11 0.00
12 0.00
13 0.00
14 0.00
15 0.00
16 0.00
17 0.00
18 0.00
19 0.00
20 0.00
21 0.00
22 0.00

@ATOM_PROPERTY
pdb_occupancy
SciTegic.value.DoubleValue
1 1.00
2 1.00
3 1.00
4 1.00
5 1.00
6 1.00
7 1.00
8 1.00
9 1.00
10 1.00
11 1.00
12 1.00
13 1.00
14 1.00
15 1.00
16 1.00
17 1.00
18 1.00
19 1.00
20 1.00
21 1.00
22 1.00

@ATOM_PROPERTY
pdb_heteroAtom
SciTegic.value.BooleanValue
1 true
2 true
3 true
4 true
5 true
6 true
7 true
8 true
9 true
10 true
11 true
12 true
13 true
14 true
15 true
16 true
17 true
18 true
19 true
20 true
21 true
22 true

You tell the script to look for a residue named

but your stream file actually contains

So your residue name is “All-At”

You’re also using an ancient version of CGenFF and the C36 port, which I strongly discourage. The current version of CGenFF is 4.4. There have been many improvements to the force field in the last several years between version 3.0.1 and 4.4.

Thank you very much for the fast answer! Ah, now I understand better, how the point about the residue name is meant. It works now!