CGenFF problem in replicating the tutorial

User discussions
1

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

2

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.

3

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

4

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.

5

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/) 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/.
Thanks for the information
Mario

6

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).