Issue in convertion of pdb to gro file in the case of ligand

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1

GROMACS version:
GROMACS modification: Yes/No
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I got error in the conversion of pdb file of ligand to .gro file. I got a converted file but which is different from yours. When I compared your file with my file,the decimal spacing is mismatched.

Glycine aRginine prOline Methionine Alanine Cystine Serine
22
0jz4. C4 1 2.400 29.400 12.400
0jz4. C7 2 2.100 55.300 21.400
0jz4. C8 3 2.200 6.800 74.700
0jz4. C9 4 2.200 67.100 51.200
0jz4. C10 5 2.200 76.900 73.000
0jz4. C11 6 2.100 69.300 45.900
0jz4. C12 7 2.200 29.400 18.700
0jz4. C13 8 2.200 46.300 41.400
0jz4. C14 9 2.300 92.500 70.400
0jz4. OAB 10 2.300 41.200 53.600
0jz4. H1 11 2.500 31.300 36.200
0jz4. H2 12 2.300 65.900 53.300
0jz4. H3 13 2.400 17.400 6.100
0jz4. H4 14 2.100 6.700 12.400
0jz4. H5 15 2.100 99.300 34.700
0jz4. H6 16 2.300 3.600 17.800
0jz4. H7 17 2.100 37.000 81.400
0jz4. H8 18 2.100 77.900 75.500
0jz4. H9 19 2.200 26.600 36.900
0jz4. H10 20 2.400 57.600 29.300
0jz4. H11 21 2.400 2.400 76.600
0jz4. H12 22 2.300 73.900 21.200
0.00000 0.00000 0.00000

This is my converted file.
Also I got a warning message in topology creation of ligand step.
python cgenff_charmm2gmx_py2.py jz4.pdb jz4_fix.mol2 jz4.str charmm36-jul2022.ff
NOTE 1: Code tested with python 2.7.12. Your version: 2.7.12 | packaged by conda-forge | (default, Feb 9 2017, 14:36:30)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]

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.str : 4.6
–Version of CGenFF detected in charmm36-jul2022.ff/forcefield.doc : 4.6

NOTE 3: To avoid duplicated parameters, do NOT select the ‘Include parameters that are already in CGenFF’ option when uploading a molecule into CGenFF.
============ DONE ============
Conversion complete.
The molecule topology has been written to jz4.pdb.itp
Additional parameters needed by the molecule are written to jz4.pdb.prm, which needs to be included in the system .top

PLEASE NOTE: lone pair construction requires duplicate host atom numbers, which will make grompp complain
To produce .tpr files, the user MUST use -maxwarn 1 to circumvent this check
============ DONE ============
what does this maxwarn indicate? Is there any issue occur when i proceed with my files I got from these steps?

2

The residue name should be JZ4, not jz4.pdb, so that is odd. But the script produces a PDB file, not a GRO file, so you’ll have to explain what you did afterwards. The coordinates look totally wrong.

3

Thank you for your reply. For the creation of ligand topology, first I created mol2 file from pdb by using open babel.
babel jz4.pdb jz4.mol2 -h (command used)
Then I deleted the 167 from the JZ4167 in the mol2 file and then sorted the bond order by the perl script you provided in your gromacs tutorial website. Then I upload that mol2 file in Cgenn server and save the str file I got from the server.
Then by using this command
python cgenff_charmm2gmx.py JZ4.pdb jz4_fix.mol2 jz4.str charmm36-jul2022.ff
I create the topology file. Here I used JZ4.pdb, because in my mol2 file instead of ***** I got JZ4.pdb when I use open babel for conversion. If I put JZ4, the I got error like the JZ4 didn’t match with my file. Then I create topology file and after that I tried to convert jz4.pdb.ini.pdb to gro file. Then I got this file.The coordinates is different from your file.

ATOM 1 C4 jz4.pdb 1 24.294 -24.124 -0.071 1.00 0.00
ATOM 2 C7 jz4.pdb 1 21.553 -27.214 -4.112 1.00 0.00
ATOM 3 C8 jz4.pdb 1 22.068 -26.747 -5.331 1.00 0.00
ATOM 4 C9 jz4.pdb 1 22.671 -25.512 -5.448 1.00 0.00
ATOM 5 C10 jz4.pdb 1 22.769 -24.730 -4.295 1.00 0.00
ATOM 6 C11 jz4.pdb 1 21.693 -26.459 -2.954 1.00 0.00
ATOM 7 C12 jz4.pdb 1 22.294 -25.187 -3.075 1.00 0.00
ATOM 8 C13 jz4.pdb 1 22.463 -24.414 -1.808 1.00 0.00
ATOM 9 C14 jz4.pdb 1 23.925 -24.704 -1.394 1.00 0.00
ATOM 10 OAB jz4.pdb 1 23.412 -23.536 -4.342 1.00 0.00
ATOM 11 H1 jz4.pdb 1 25.313 -24.362 0.151 1.00 0.00
ATOM 12 H2 jz4.pdb 1 23.659 -24.533 0.687 1.00 0.00
ATOM 13 H3 jz4.pdb 1 24.174 -23.061 -0.102 1.00 0.00
ATOM 14 H4 jz4.pdb 1 21.067 -28.124 -4.075 1.00 0.00
ATOM 15 H5 jz4.pdb 1 21.993 -27.347 -6.167 1.00 0.00
ATOM 16 H6 jz4.pdb 1 23.036 -25.178 -6.354 1.00 0.00
ATOM 17 H7 jz4.pdb 1 21.370 -26.814 -2.041 1.00 0.00
ATOM 18 H8 jz4.pdb 1 21.779 -24.755 -1.059 1.00 0.00
ATOM 19 H9 jz4.pdb 1 22.266 -23.369 -1.930 1.00 0.00
ATOM 20 H10 jz4.pdb 1 24.576 -24.293 -2.138 1.00 0.00
ATOM 21 H11 jz4.pdb 1 24.024 -25.766 -1.311 1.00 0.00
ATOM 22 H12 jz4.pdb 1 23.739 -23.212 -5.158 1.00 0.00
END

This is my jz4.pdb.ini.pdb file.