All bonds in the 1,2 butane diol molecule are being lost after the conversion in CGenFF

User discussions
1

GROMACS version:2021.1
GROMACS modification: No
Hello dear collegues,
I have to use the diol molecules as solvent in MD simulation to see its effect on protein. for that i have downloaded the sdf file fro pubchem and converted it to mol2 file using the Convert application on browser. after that I have used cgenff (User Login) to get the str file. and further i have converted the str file with the python script to get the itp, prm, pdb and top file. when i am viewing the pdb file in pymol all bond s are lost. but in mol2 file its showing all the bonds. i have to idea how to solve this problem. please help me with this. i am attaching the files for the reference
mol2 file

@MOLECULE
12BDO
16 15 1
SMALL
USER_CHARGES
@ATOM
1 O1 0.0162 1.3482 0.2382 O.3 1 noname -0.3906
2 O2 2.4354 0.0159 -0.2142 O.3 1 noname -0.3936
3 C1 0.0209 0.0134 -0.2675 C.3 1 noname 0.0769
4 C2 -1.2400 -0.7032 0.2195 C.3 1 noname -0.0276
5 C3 1.2812 -0.6925 0.2255 C.3 1 noname 0.0692
6 C4 -2.5137 0.0181 -0.2016 C.3 1 noname -0.0628
7 H1 0.0256 0.0817 -1.3613 H 1 noname 0.0624
8 H2 -1.2341 -0.7647 1.3147 H 1 noname 0.0291
9 H3 -1.2580 -1.7282 -0.1681 H 1 noname 0.0291
10 H4 1.3164 -0.7098 1.3196 H 1 noname 0.0590
11 H5 1.3386 -1.7210 -0.1441 H 1 noname 0.0590
12 H6 -2.5749 1.0170 0.2415 H 1 noname 0.0231
13 H7 -2.5640 0.1195 -1.2903 H 1 noname 0.0231
14 H8 -3.3917 -0.5471 0.1270 H 1 noname 0.0231
15 H9 0.8324 1.7786 -0.0690 H 1 noname 0.2105
16 H10 2.4163 0.0294 -1.1863 H 1 noname 0.2101
@BOND
1 1 3 1
2 1 15 1
3 2 5 1
4 2 16 1
5 3 4 1
6 3 5 1
7 3 7 1
8 4 6 1
9 4 8 1
10 4 9 1
11 5 10 1
12 5 11 1
13 6 12 1
14 6 13 1
15 6 14 1
@SUBSTRUCTURE
1 noname 1

str file

  • Toppar stream file generated by
  • CHARMM General Force Field (CGenFF) program version 2.5
  • For use with CGenFF version 4.5

read rtf card append

  • Topologies generated by
  • CHARMM General Force Field (CGenFF) program version 2.5

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 12BDO 0.000 ! param penalty= 0.600 ; charge penalty= 0.298
GROUP ! CHARGE CH_PENALTY
ATOM O1 OG311 -0.646 ! 0.000
ATOM O2 OG311 -0.649 ! 0.000
ATOM C1 CG311 0.127 ! 0.283
ATOM C2 CG321 -0.182 ! 0.298
ATOM C3 CG321 0.063 ! 0.030
ATOM C4 CG331 -0.271 ! 0.239
ATOM H1 HGA1 0.090 ! 0.000
ATOM H2 HGA2 0.090 ! 0.000
ATOM H3 HGA2 0.090 ! 0.000
ATOM H4 HGA2 0.090 ! 0.000
ATOM H5 HGA2 0.090 ! 0.000
ATOM H6 HGA3 0.090 ! 0.000
ATOM H7 HGA3 0.090 ! 0.000
ATOM H8 HGA3 0.090 ! 0.000
ATOM H9 HGP1 0.419 ! 0.000
ATOM H10 HGP1 0.419 ! 0.000

BOND O1 C1
BOND O1 H9
BOND O2 C3
BOND O2 H10
BOND C1 C2
BOND C1 C3
BOND C1 H1
BOND C2 C4
BOND C2 H2
BOND C2 H3
BOND C3 H4
BOND C3 H5
BOND C4 H6
BOND C4 H7
BOND C4 H8

END

read param card flex append

  • Parameters generated by analogy by
  • CHARMM General Force Field (CGenFF) program version 2.5

! 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 CG311 CG321 CG331 0.2000 3 0.00 ! 11429 , from CG311 CG311 CG321 CG331, penalty= 0.6

IMPROPERS

END
RETURN

pdb file

ATOM 1 O1 12BDO 1 0.016 1.348 0.238 1.00 0.00
ATOM 2 O2 12BDO 1 2.435 0.016 -0.214 1.00 0.00
ATOM 3 C1 12BDO 1 0.021 0.013 -0.268 1.00 0.00
ATOM 4 C2 12BDO 1 -1.240 -0.703 0.220 1.00 0.00
ATOM 5 C3 12BDO 1 1.281 -0.693 0.226 1.00 0.00
ATOM 6 C4 12BDO 1 -2.514 0.018 -0.202 1.00 0.00
ATOM 7 H1 12BDO 1 0.026 0.082 -1.361 1.00 0.00
ATOM 8 H2 12BDO 1 -1.234 -0.765 1.315 1.00 0.00
ATOM 9 H3 12BDO 1 -1.258 -1.728 -0.168 1.00 0.00
ATOM 10 H4 12BDO 1 1.316 -0.710 1.320 1.00 0.00
ATOM 11 H5 12BDO 1 1.339 -1.721 -0.144 1.00 0.00
ATOM 12 H6 12BDO 1 -2.575 1.017 0.241 1.00 0.00
ATOM 13 H7 12BDO 1 -2.564 0.119 -1.290 1.00 0.00
ATOM 14 H8 12BDO 1 -3.392 -0.547 0.127 1.00 0.00
ATOM 15 H9 12BDO 1 0.832 1.779 -0.069 1.00 0.00
ATOM 16 H10 12BDO 1 2.416 0.029 -1.186 1.00 0.00
END

please help me with this.

2

Hi. Did you find out why that happened? Was your output something like this? I think I am facing the exact same issue. This is how the .gro file looks. It was perfectly fine before cgenff.

image

3

Hi, some errors like this stem from faulty formatting of the .gro file, such as too few blank spaces. Compare field widths to a working .gro file from elsewhere to make sure this is not the issue.

4

Hi. The solution is here. My ligand name was 5 characters long. Problem in file (Broken structure ini.pdb) generated using CGenFF for proceeding in MD Simulation - User discussions - GROMACS forums (bioexcel.eu)

I am going to play around with the conversion script and see if I can address this differently.

5

It should be a simple matter of truncating any residue name at 4 characters. I thought we had done this years ago but I guess not. I have other things to fix and update in the script. I’ll add this to the list.

1 Like
6

Yes the ini.pdb gives the broken structure. So I used the .mol2 file and converted it to pdb and the file I used to get the grow file