# CGenFF problem in replicating the tutorial **URL:** \ **Category:** User discussions\ **Created:** [July 16, 2021, 9:06pm UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522 "2021-07-16T21:06:48Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![itsrdclab](https://avatars.discourse-cdn.com/v4/letter/i/898d66/32.png) [@itsrdclab](https://gromacs.bioexcel.eu/u/itsrdclab)\ **Post date:** [July 16, 2021, 9:06pm UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/1 "2021-07-16T21:06:48Z")
Hi all, I am new in GROMACS and I just started learning the preparation of the protein and ligand for MD simulation. I used the tutorial using JZ4 and the tutorial specified that I needed to upload the fixed mol2 file using the perl script to convert it to str file. Regardless if I use the legacy or the latest CGenFF versions, the str file generated by the server was different from the one that was uploaded in the website. I received the following error when I used the str file generated by the server: – NOTE 1: Code tested with python 3.5.2. Your version: 3.7.7 (default, May 7 2020, 21:25:33) [GCC 7.3.0] NOTE 2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: –Version of CGenFF detected in jz4\_fix.str : 4.4 –Version of CGenFF detected in charmm36-mar2019.ff/forcefield.doc : 4.1 WARNING: CGenFF versions are not equivalent! NOTE 3: 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 – But when I used the str file downloaded from the tutorial, the conversion to itp was successful. I am placing below the str file generated by the CGenFF for your reference. – - 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 jz4 0.000 ! param penalty= 0.900 ; charge penalty= 0.342 GROUP ! CHARGE CH\_PENALTY ATOM C4 CG331 -0.271 ! 0.285 ATOM C7 CG2R61 -0.108 ! 0.000 ATOM C8 CG2R61 -0.112 ! 0.000 ATOM C9 CG2R61 -0.110 ! 0.000 ATOM C10 CG2R61 0.103 ! 0.030 ATOM C11 CG2R61 -0.115 ! 0.000 ATOM C12 CG2R61 -0.007 ! 0.218 ATOM C13 CG321 -0.178 ! 0.342 ATOM C14 CG321 -0.183 ! 0.045 ATOM OAB OG311 -0.529 ! 0.190 ATOM H1 HGA3 0.090 ! 0.000 ATOM H2 HGA3 0.090 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGR61 0.115 ! 0.000 ATOM H5 HGR61 0.115 ! 0.000 ATOM H6 HGR61 0.115 ! 0.000 ATOM H7 HGR61 0.115 ! 0.000 ATOM H8 HGA2 0.090 ! 0.000 ATOM H9 HGA2 0.090 ! 0.000 ATOM H10 HGA2 0.090 ! 0.000 ATOM H11 HGA2 0.090 ! 0.000 ATOM H12 HGP1 0.420 ! 0.000 BOND C4 C14 BOND C4 H1 BOND C4 H2 BOND C4 H3 BOND C7 C8 BOND C7 C11 BOND C7 H4 BOND C8 C9 BOND C8 H5 BOND C9 C10 BOND C9 H6 BOND C10 OAB BOND C10 C12 BOND C11 C12 BOND C11 H7 BOND C12 C13 BOND C13 C14 BOND C13 H8 BOND C13 H9 BOND C14 H10 BOND C14 H11 BOND OAB H12 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 CG321 CG2R61 CG2R61 OG311 2.4000 2 180.00 ! jz4 , from CG311 CG2R61 CG2R61 OG311, penalty= 0.6 CG2R61 CG321 CG321 CG331 0.0400 3 0.00 ! jz4 , from CG2R61 CG321 CG321 CG321, penalty= 0.9 IMPROPERS END RETURN – Can somebody explain where the problem lies? Thank you. Joanna ---
**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:** [July 20, 2021, 1:16pm UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/2 "2021-07-20T13:16:35Z")
Download the latest version of the C36 port and it will have the correct matching CGenFF version. The output may differ slightly from that of the tutorial (which was written a few years ago, for different versions), but the procedure is still the same. ---
**Author:** ![lek](https://avatars.discourse-cdn.com/v4/letter/l/7ea924/32.png) [@lek](https://gromacs.bioexcel.eu/u/lek)\ **Post date:** [October 30, 2021, 2:10am UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/3 "2021-10-30T02:10:17Z")
Sir, I have downloaded the latest charmm36-feb2021.ff port which is having Cgenff version 4.4 in forcefield .doc file . but the .str file generated from the CGENFF program is having cgenff version 4.5. hence showing error. how to resolve this issue. kindly help ---
**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:** [November 1, 2021, 3:39am UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/4 "2021-11-01T03:39:52Z")
For the purpose of completing the tutorial, it should suffice to simply comment out the version check in the conversion script. I don’t recommend that in general but I doubt there are any conflicts that are relevant in such a simple molecule. ---
**Author:** ![squinzanetto](https://avatars.discourse-cdn.com/v4/letter/s/858c86/32.png) [@squinzanetto](https://gromacs.bioexcel.eu/u/squinzanetto)\ **Post date:** [November 24, 2023, 1:34am UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/5 "2023-11-24T01:34:01Z")
ir, I just ned to know if there is a standalone version of cgenff that can be downloaded (which works like the server at [https://cgenff.silcsbio.com/](https://cgenff.silcsbio.com/)) or if it suffices to use charmm-gui to get the str files required to preceed acoording to the tutorial at [http://www.mdtutorials.com/](http://www.mdtutorials.com/). Thanks for the information Mario ---
**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 7, 2023, 2:46pm UTC](https://gromacs.bioexcel.eu/t/cgenff-problem-in-replicating-the-tutorial/2522/6 "2023-12-07T14:46:07Z")
You can license a CGenFF binary from SilcsBio, LLC (free for academic use). Otherwise, topologies can be generated via the CGenFF server or CHARMM-GUI (which is just sending your molecule to the CGenFF server).