# CGenff Error: specified residue name does not match between str and mol2 files **URL:** \ **Category:** User discussions\ **Created:** [December 3, 2020, 10:23am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190 "2020-12-03T10:23:53Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Maggie](https://avatars.discourse-cdn.com/v4/letter/m/9d8465/32.png) [@Maggie](https://gromacs.bioexcel.eu/u/Maggie)\ **Post date:** [December 3, 2020, 10:23am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/1 "2020-12-03T10:23:54Z")
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](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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 4, 2020, 1:55am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/2 "2020-12-04T01:55:01Z")
You tell the script to look for a residue named > [@Maggie](#): > > TETRAMATHYLP but your stream file actually contains > [@Maggie](#): > > RESI All-At 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. ---
**Author:** ![Maggie](https://avatars.discourse-cdn.com/v4/letter/m/9d8465/32.png) [@Maggie](https://gromacs.bioexcel.eu/u/Maggie)\ **Post date:** [December 4, 2020, 8:57am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/3 "2020-12-04T08:57:50Z")
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! ---
**Author:** ![Amey](https://avatars.discourse-cdn.com/v4/letter/a/a8b319/32.png) [@Amey](https://gromacs.bioexcel.eu/u/Amey)\ **Post date:** [April 23, 2023, 6:46pm UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/4 "2023-04-23T18:46:45Z")
Thanks!!! ---
**Author:** ![Sonia](https://avatars.discourse-cdn.com/v4/letter/s/c67d28/32.png) [@Sonia](https://gromacs.bioexcel.eu/u/Sonia)\ **Post date:** [December 3, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/5 "2024-12-03T06:39:40Z")
Hi, I am getting similar error. Were you able to troubleshoot this? Can you please help? ---
**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:** [March 1, 2025, 10:35am UTC](https://gromacs.bioexcel.eu/t/cgenff-error-specified-residue-name-does-not-match-between-str-and-mol2-files/1190/6 "2025-03-01T10:35:56Z")
make ligand name of 3 letter in mol2 file then you can go for ligand\_fix.mol2 and then .str