Hello all,
We have tried using the server several times and followed the instructions but could not get the parameters for our structures. Please, can you help to generate oplsaa parameters for attached structures?
The structures are canonicalised and the net charge for each structure is zero.
Thanks
Mohammed
complexes.zip

Hi,
I used LigParGen locally and I have encounter an error like this with my system:

$ LigParGen -p opt.pdb -r UNL -c 0 -o 0
Warning!!
1.Cannonicalising Input MOL/PDB file
2.Atom ordering may change
3.But the Coordinates remain the same
1 molecule converted
31 audit log messages
1 molecule converted
31 audit log messages
MOLECULE HAS A CHARGE of 0
Traceback (most recent call last):
File "/vol/home/calvanid/anaconda2/bin/LigParGen", line 10, in
sys.exit(main())
File "/vol/home/calvanid/anaconda2/lib/python2.7/site-packages/LigParGen/Converter.py", line 90, in main
convert(**vars(args))
File "/vol/home/calvanid/anaconda2/lib/python2.7/site-packages/LigParGen/Converter.py", line 159, in convert
), "Hydrogens are not added. Please add Hydrogens"
AssertionError: Hydrogens are not added. Please add Hydrogens

It's a molecule with only 30 atoms carbon atoms, but without hydrogens and fluorine atoms in their place.

Do you have any advice to solve this problem?

Thanks a lot for your time and waiting for your kind reply,

My Best Regards

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version: For BOSS, OpenMM and Gromacs
Method: Extra sites and Lone Pairs

Expected Behavior

Actual Behavior

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version : http://zarbi.chem.yale.edu/ligpargen/
Method: Not relevant (1.14*CM1A for charges, if it matters)

Expected Behavior

We would like LibParGen to report the atom type strings that it uses for force-field lookup in the files that it creates. I am specifically asking for the atom type names that are used for looking up force-field parameters in the official OPLSAA files (distributed here and here). These atoms have names like "C135", "C137", "C283", "H140" (not "CA" or "C01". Those are PDB atom-names. That's not what we need.)

I explain why this would be very useful below.

It would be great if all of the files generated by LibParGen included these atom type names, but we would be happy to settle for Charmm RTF and PRM files for now. (OpenMM/FF XML and LAMMPS would be great too.)

I'd also request the the output files include a time and date. The reason I ask this is because it is important to know which version of the OPLSAA force field was used, and this can (hopefully) be inferred from the date. (I suspect that these atom type strings might vary depending on the version of OPLSAA you are using. If so, perhaps you could include the date somewhere in the headers of the files you create? Or in the file names?)

Actual Behavior

Currently each atom is assigned to a unique (automatically generated) type name even if there are multiple copies of the same atom in the molecule.

Also, if you run LibParGen twice on two different molecules, there is a high chance that they will both contain an atom of type "C801" (for example), even though (I suspect) that atom type probably refers to something different in those two molecules. This makes it hard to combine two different molecules in the same simulation.

Benefits of revealing atom types

1. Allow users to combine multiple different molecules together in the same simulation without having to worry about atom type name collisions.
2. Reduce the number of questions you receive from users wondering why LibParGen generated a molecule with unexpected force field parameters. (I see many issues like this on the issue-tracker.) LibParGen is currently a black box. Let users look inside the box (a little bit) and answer their own questions.
3. Make it easier for third-party developers (such as myself) to write tools which can convert LibParGen output files into new formats.

I'm currently trying to release a tool which will convert LibParGen into moltemplate format. This will make it significantly easier for LAMMPS users to benefit from LibParGen. (Moltemplate is a molecule-builder for LAMMPS. I wrote moltemplate.) Hiding the atom type makes this task much harder.

Is there a reason atom types are hidden? Are there some atom types generated by LibParGen that do not correspond to anything that's in the OPLSAA force field files? (If that is the case, would you be willing to consider reporting the atom type names for the subset of atoms which are defined in the official OPLSAA files?)

Thanks in advance for your time and consideration.

Need to improve the PDB files generated by LigParGen.

I have a molecule with 66 atoms for which I need the opls-aa topology file. But unfortunately, LigPargen isn't accepting the PDB file. Kindly look into it.

The following is the PDB

COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.4.1
HETATM 1 CP UNL 1 6.750 1.190 0.863 1.00 0.00 C
HETATM 2 HP UNL 1 5.981 0.745 1.451 1.00 0.00 H
HETATM 3 CL UNL 1 7.379 2.349 1.238 1.00 0.00 C
HETATM 4 HL UNL 1 7.109 2.817 2.161 1.00 0.00 H
HETATM 5 CK UNL 1 8.345 2.892 0.408 1.00 0.00 C
HETATM 6 HK UNL 1 8.845 3.798 0.682 1.00 0.00 H
HETATM 7 CL UNL 1 8.662 2.253 -0.784 1.00 0.00 C
HETATM 8 HL UNL 1 9.401 2.646 -1.448 1.00 0.00 H
HETATM 9 CP UNL 1 8.009 1.097 -1.108 1.00 0.00 C
HETATM 10 HP UNL 1 8.212 0.562 -2.011 1.00 0.00 H
HETATM 11 NP UNL 1 7.073 0.577 -0.290 1.00 0.00 N
HETATM 12 CN UNL 1 6.368 -0.675 -0.670 1.00 0.00 C
HETATM 13 HN UNL 1 6.731 -1.014 -1.626 1.00 0.00 H
HETATM 14 HN UNL 1 6.566 -1.439 0.069 1.00 0.00 H
HETATM 15 CE UNL 1 4.867 -0.438 -0.758 1.00 0.00 C
HETATM 16 OE UNL 1 4.314 0.540 -0.326 1.00 0.00 O
HETATM 17 OA UNL 1 4.314 -1.488 -1.329 1.00 0.00 O
HETATM 18 CA UNL 1 2.838 -1.599 -1.510 1.00 0.00 C
HETATM 19 HA UNL 1 2.392 -0.704 -1.121 1.00 0.00 H
HETATM 20 HA UNL 1 2.696 -1.659 -2.577 1.00 0.00 H
HETATM 21 C2 UNL 1 2.378 -2.870 -0.805 1.00 0.00 C
HETATM 22 H2 UNL 1 1.328 -3.017 -1.031 1.00 0.00 H
HETATM 23 H2 UNL 1 2.921 -3.697 -1.244 1.00 0.00 H
HETATM 24 C2 UNL 1 2.595 -2.873 0.726 1.00 0.00 C
HETATM 25 H2 UNL 1 2.675 -3.908 1.040 1.00 0.00 H
HETATM 26 H2 UNL 1 3.551 -2.412 0.954 1.00 0.00 H
HETATM 27 C2 UNL 1 1.483 -2.218 1.579 1.00 0.00 C
HETATM 28 H2 UNL 1 0.539 -2.698 1.345 1.00 0.00 H
HETATM 29 H2 UNL 1 1.698 -2.459 2.615 1.00 0.00 H
HETATM 30 C2 UNL 1 1.337 -0.677 1.444 1.00 0.00 C
HETATM 31 H2 UNL 1 2.273 -0.246 1.107 1.00 0.00 H
HETATM 32 H2 UNL 1 1.141 -0.255 2.424 1.00 0.00 H
HETATM 33 C2 UNL 1 0.186 -0.233 0.508 1.00 0.00 C
HETATM 34 H2 UNL 1 0.218 -0.793 -0.422 1.00 0.00 H
HETATM 35 H2 UNL 1 0.316 0.816 0.257 1.00 0.00 H
HETATM 36 C2 UNL 1 -1.204 -0.414 1.149 1.00 0.00 C
HETATM 37 H2 UNL 1 -1.350 -1.451 1.433 1.00 0.00 H
HETATM 38 H2 UNL 1 -1.252 0.178 2.059 1.00 0.00 H
HETATM 39 C2 UNL 1 -2.345 0.014 0.205 1.00 0.00 C
HETATM 40 H2 UNL 1 -2.203 1.053 -0.081 1.00 0.00 H
HETATM 41 H2 UNL 1 -2.301 -0.579 -0.704 1.00 0.00 H
HETATM 42 C2 UNL 1 -3.734 -0.149 0.850 1.00 0.00 C
HETATM 43 H2 UNL 1 -3.877 -1.188 1.137 1.00 0.00 H
HETATM 44 H2 UNL 1 -3.780 0.445 1.758 1.00 0.00 H
HETATM 45 C2 UNL 1 -4.875 0.278 -0.093 1.00 0.00 C
HETATM 46 H2 UNL 1 -4.831 -0.317 -1.001 1.00 0.00 H
HETATM 47 H2 UNL 1 -4.734 1.316 -0.380 1.00 0.00 H
HETATM 48 C2 UNL 1 -6.265 0.115 0.552 1.00 0.00 C
HETATM 49 H2 UNL 1 -6.407 -0.923 0.839 1.00 0.00 H
HETATM 50 H2 UNL 1 -6.310 0.710 1.460 1.00 0.00 H
HETATM 51 C2 UNL 1 -7.406 0.542 -0.391 1.00 0.00 C
HETATM 52 H2 UNL 1 -7.264 1.580 -0.678 1.00 0.00 H
HETATM 53 H2 UNL 1 -7.362 -0.053 -1.299 1.00 0.00 H
HETATM 54 C2 UNL 1 -8.796 0.379 0.255 1.00 0.00 C
HETATM 55 H2 UNL 1 -8.841 0.974 1.163 1.00 0.00 H
HETATM 56 H2 UNL 1 -8.938 -0.659 0.542 1.00 0.00 H
HETATM 57 C2 UNL 1 -9.937 0.806 -0.688 1.00 0.00 C
HETATM 58 H2 UNL 1 -9.893 0.212 -1.597 1.00 0.00 H
HETATM 59 H2 UNL 1 -9.796 1.845 -0.976 1.00 0.00 H
HETATM 60 C2 UNL 1 -11.327 0.644 -0.045 1.00 0.00 C
HETATM 61 H2 UNL 1 -11.470 -0.393 0.242 1.00 0.00 H
HETATM 62 H2 UNL 1 -11.373 1.238 0.863 1.00 0.00 H
HETATM 63 C3 UNL 1 -12.459 1.075 -0.998 1.00 0.00 C
HETATM 64 H3 UNL 1 -13.430 0.954 -0.529 1.00 0.00 H
HETATM 65 H3 UNL 1 -12.444 0.476 -1.903 1.00 0.00 H
HETATM 66 H3 UNL 1 -12.346 2.116 -1.279 1.00 0.00 H
CONECT 1 11 3 2
CONECT 2 1
CONECT 3 5 1 4
CONECT 4 3
CONECT 5 7 6 3
CONECT 6 5
CONECT 7 8 9 5
CONECT 8 7
CONECT 9 10 7 11
CONECT 10 9
CONECT 11 9 12 1
CONECT 12 13 15 11 14
CONECT 13 12
CONECT 14 12
CONECT 15 17 12 16
CONECT 16 15
CONECT 17 18 15
CONECT 18 20 17 19 21
CONECT 19 18
CONECT 20 18
CONECT 21 18 23 22 24
CONECT 22 21
CONECT 23 21
CONECT 24 21 26 25 27
CONECT 25 24
CONECT 26 24
CONECT 27 24 28 30 29
CONECT 28 27
CONECT 29 27
CONECT 30 33 31 27 32
CONECT 31 30
CONECT 32 30
CONECT 33 34 35 36 30
CONECT 34 33
CONECT 35 33
CONECT 36 39 33 37 38
CONECT 37 36
CONECT 38 36
CONECT 39 41 40 42 36
CONECT 40 39
CONECT 41 39
CONECT 42 45 39 43 44
CONECT 43 42
CONECT 44 42
CONECT 45 46 47 48 42
CONECT 46 45
CONECT 47 45
CONECT 48 51 45 49 50
CONECT 49 48
CONECT 50 48
CONECT 51 53 52 54 48
CONECT 52 51
CONECT 53 51
CONECT 54 57 51 56 55
CONECT 55 54
CONECT 56 54
CONECT 57 58 59 60 54
CONECT 58 57
CONECT 59 57
CONECT 60 63 57 61 62
CONECT 61 60
CONECT 62 60
CONECT 63 65 66 64 60
CONECT 64 63
CONECT 65 63
CONECT 66 63
MASTER 0 0 0 0 0 0 0 0 66 0 66 0
END

ATOM 1 O7N NAD B 1 -18.523 -4.437 19.312 1.00 20.63 O
ATOM 2 C7N NAD B 1 -17.694 -4.517 20.210 1.00 18.83 C
ATOM 3 N7N NAD B 1 -17.811 -5.407 21.166 1.00 17.32 N
ATOM 4 C3N NAD B 1 -16.483 -3.628 20.286 1.00 20.16 C
ATOM 5 C2N NAD B 1 -16.195 -2.692 19.289 1.00 19.75 C
ATOM 6 C4N NAD B 1 -15.636 -3.750 21.393 1.00 19.70 C
ATOM 7 C5N NAD B 1 -14.514 -2.925 21.460 1.00 20.05 C
ATOM 8 C6N NAD B 1 -14.295 -2.018 20.447 1.00 19.43 C
ATOM 9 N1N NAD B 1 -15.115 -1.918 19.392 1.00 19.62 N
ATOM 10 C1D NAD B 1 -14.817 -0.919 18.351 1.00 20.78 C
ATOM 11 O4D NAD B 1 -15.851 0.090 18.277 1.00 21.86 O
ATOM 12 C2D NAD B 1 -14.764 -1.522 16.947 1.00 21.58 C
ATOM 13 O2D NAD B 1 -13.484 -2.031 16.541 1.00 21.48 O
ATOM 14 C3D NAD B 1 -15.105 -0.330 16.083 1.00 21.22 C
ATOM 15 O3D NAD B 1 -13.907 0.455 15.899 1.00 19.57 O
ATOM 16 C4D NAD B 1 -16.125 0.419 16.900 1.00 22.26 C
ATOM 17 C5D NAD B 1 -17.557 0.079 16.495 1.00 23.21 C
ATOM 18 O5D NAD B 1 -17.807 -1.344 16.536 1.00 24.75 O
ATOM 19 PN NAD B 1 -19.184 -1.976 16.021 1.00 25.31 P
ATOM 20 O1N NAD B 1 -19.202 -3.447 16.443 1.00 26.69 O
ATOM 21 O2N NAD B 1 -20.349 -1.107 16.369 1.00 27.24 O
ATOM 22 O3 NAD B 1 -19.006 -2.087 14.411 1.00 28.73 O
ATOM 23 PA NAD B 1 -20.128 -2.426 13.310 1.00 31.17 P
ATOM 24 O1A NAD B 1 -21.551 -2.538 13.821 1.00 30.16 O
ATOM 25 O2A NAD B 1 -19.612 -3.447 12.320 1.00 28.35 O
ATOM 26 O5B NAD B 1 -20.075 -1.006 12.558 1.00 31.82 O
ATOM 27 C5B NAD B 1 -18.816 -0.554 12.057 1.00 30.72 C
ATOM 28 C4B NAD B 1 -19.049 0.374 10.871 1.00 28.82 C
ATOM 29 C3B NAD B 1 -19.841 -0.321 9.761 1.00 28.18 C
ATOM 30 O3B NAD B 1 -21.013 0.442 9.436 1.00 25.57 O
ATOM 31 C2B NAD B 1 -18.837 -0.435 8.623 1.00 27.56 C
ATOM 32 O2B NAD B 1 -19.405 -0.439 7.303 1.00 27.24 O
ATOM 33 C1B NAD B 1 -17.952 0.757 8.888 1.00 25.97 C
ATOM 34 O4B NAD B 1 -17.799 0.780 10.306 1.00 28.40 O
ATOM 35 N9A NAD B 1 -16.635 0.680 8.228 1.00 26.46 N
ATOM 36 C4A NAD B 1 -16.086 1.741 7.611 1.00 25.86 C
ATOM 37 C5A NAD B 1 -14.800 1.255 7.098 1.00 24.87 C
ATOM 38 N7A NAD B 1 -14.683 -0.051 7.457 1.00 25.31 N
ATOM 39 C8A NAD B 1 -15.797 -0.389 8.147 1.00 24.16 C
ATOM 40 N3A NAD B 1 -16.482 3.039 7.403 1.00 23.82 N
ATOM 41 C2A NAD B 1 -15.696 3.881 6.730 1.00 24.89 C
ATOM 42 N1A NAD B 1 -14.492 3.512 6.244 1.00 27.37 N
ATOM 43 C6A NAD B 1 -13.990 2.243 6.375 1.00 26.56 C
ATOM 44 N6A NAD B 1 -12.785 1.895 5.860 1.00 27.54 N
ATOM 45 H7N1 NAD B 1 -17.116 -5.457 21.898 1.00 0.00 H
ATOM 46 H7N2 NAD B 1 -18.596 -6.043 21.171 1.00 0.00 H
ATOM 47 H2N NAD B 1 -16.848 -2.595 18.434 1.00 0.00 H
ATOM 48 H4N NAD B 1 -15.859 -4.469 22.167 1.00 0.00 H
ATOM 49 H5N NAD B 1 -13.835 -3.004 22.296 1.00 0.00 H
ATOM 50 H6N NAD B 1 -13.440 -1.359 20.488 1.00 0.00 H
ATOM 51 H1D NAD B 1 -13.863 -0.441 18.574 1.00 0.00 H
ATOM 52 H2D NAD B 1 -15.526 -2.294 16.840 1.00 0.00 H
ATOM 53 HO2D NAD B 1 -13.548 -2.387 15.652 1.00 0.00 H
ATOM 54 H3D NAD B 1 -15.521 -0.644 15.126 1.00 0.00 H
ATOM 55 HO3D NAD B 1 -14.105 1.218 15.351 1.00 0.00 H
ATOM 56 H4D NAD B 1 -15.967 1.488 16.759 1.00 0.00 H
ATOM 57 H5D1 NAD B 1 -17.747 0.452 15.489 1.00 0.00 H
ATOM 58 H5D2 NAD B 1 -18.253 0.589 17.161 1.00 0.00 H
ATOM 59 HO2N NAD B 1 -21.158 -1.512 16.048 1.00 0.00 H
ATOM 60 HO2A NAD B 1 -20.294 -3.637 11.671 1.00 0.00 H
ATOM 61 H5B1 NAD B 1 -18.224 -1.411 11.736 1.00 0.00 H
ATOM 62 H5B2 NAD B 1 -18.286 -0.014 12.842 1.00 0.00 H
ATOM 63 H4B NAD B 1 -19.596 1.255 11.206 1.00 0.00 H
ATOM 64 H3B NAD B 1 -20.134 -1.318 10.091 1.00 0.00 H
ATOM 65 HO3B NAD B 1 -21.502 -0.002 8.740 1.00 0.00 H
ATOM 66 H2B NAD B 1 -18.253 -1.345 8.758 1.00 0.00 H
ATOM 67 HO2B NAD B 1 -18.703 -0.514 6.652 1.00 0.00 H
ATOM 68 H1B NAD B 1 -18.464 1.664 8.566 1.00 0.00 H
ATOM 69 H8A NAD B 1 -16.074 -1.328 8.602 1.00 0.00 H
ATOM 70 H2A NAD B 1 -16.016 4.898 6.558 1.00 0.00 H
ATOM 71 H6A1 NAD B 1 -12.232 2.579 5.363 1.00 0.00 H
ATOM 72 H6A2 NAD B 1 -12.441 0.952 5.973 1.00 0.00 H
END

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :
Method:

Expected Behavior

Actual Behavior

Hello,

I have been using LigParGen to generate OPLS parameters for an organic catalyst I've been using for research, and haven't had any issues, it has been working well. I've been submitting pdb files with optimized geometries and vibrational frequencies from a computational chemistry program called WebMO.

Now I want to generate parameters for an SO4 2- molecule. I have generated a pdb file the same way from WebMO, but LPG gives me an Unknown error. I have reviewed the file in a text editor, and change the ligand from UNK to SO4, but it still isn't working. I was wondering if you could help me. Thanks!

sofour.pdb.zip

I tried uploading the file as pdb but this doesn't support it, so I've uploaded a zip file in hope that that helps. Please let me know what other information I can provide to help you. Thank you.

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :
Method:

Expected Behavior

Dear,
trying to obtain .top and .gro files from BNZ.pdb, however steadily receive an error message: Sorry, an error has been detected in your input data (file, smile or selected charge):
Found residue ligand BNZ Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code

However, when I rename the same file (for example to X.pdb or to some other name) and upload to server, everything works as expected.
For your convenience please find BNZ.pdb file (attached as BNZ.pdb.txt because GitHub does not support pdb file type).

Regards,
Dr. Drasko Tomic
BNZ.pdb.txt

Actual Behavior

• I believe this to be a bug with LigParGen
• This is a feature request

It is often difficult or impossible to track down the source of parameters and atom types, yet understanding the context in which a particular atom type or parameter was derived is essential for using a force field. It is also useful to have the original source to verify the accuracy of specific parameter values (even though I'm sure LigParGen is likely to be accurate). It would be extremely useful if LigParGen printed out some DOI references, or at least pointed the user in the direction of where parameters are derived and reported.

Hi, I want to generate parameter for attached three ligands: MDA, MDB, and MDC. However, Unknown error was reported... Would you help me fix this ?

Thanks !

MDA.pdb.gz
MDB.pdb.gz
MDC.pdb.gz

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :
Method:

Expected Behavior

Actual Behavior

[X ] I believe this to be a bug with LigParGen

Issue Information

Software name & Version : LigParGen local version

Expected Behavior

Entered the SMILES of linear molecules with a triple bond into LigParGen to receive topology and parameters. Example of SMILES: CCCC#C
LigParGen -s 'CCCC#C' -r 'CCCC#C' -c 0 -o 0 -l

Actual Behavior

Instead of a successful generation of topology files, I received the error message:
LBCC converter is activated
1 molecule converted
77 audit log messages
MOLECULE HAS A CHARGE of 0
Traceback (most recent call last):
File "/home/pchau/anaconda2/envs/my-rdkit-env/bin/LigParGen", line 10, in
sys.exit(main())
File "/home/pchau/anaconda2/envs/my-rdkit-env/lib/python3.6/site-packages/LigParGen/Converter.py", line 90, in main
convert(**vars(args))
File "/home/pchau/anaconda2/envs/my-rdkit-env/lib/python3.6/site-packages/LigParGen/Converter.py", line 144, in convert
mol = BOSSReader('%s.z' % resname, optim, charge, lbcc)
File "/home/pchau/anaconda2/envs/my-rdkit-env/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 283, in init
self.refine_data(optim, charge, lbcc)
File "/home/pchau/anaconda2/envs/my-rdkit-env/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 507, in refine_data
lbcc_MD = self.get_ImpDat(optim, charge)
File "/home/pchau/anaconda2/envs/my-rdkit-env/lib/python3.6/site-packages/LigParGen/BOSSReader.py", line 496, in get_ImpDat
sdat[impDat['ADDinit']:impDat['ADDfinal']])
KeyError: 'ADDinit'

However, I can generate the topology and parameters of this same chemical if I used the LigParGen web server instead.

Is it something wrong with my local version?

Thank you so much for your time and consideration.

Best regards,
Phuong

beta-cyclodextrin.pdb (attached gzipped) fails for unknown reason. SMILES cannot be used -- too long.

beta-cyclodextrin.pdb.gz

Feature request

Hello LigPArGen Users and @leelasd

I am trying to generate some OPLS parameters for my structure. Yes. there are two residues quite right but why can't LigPArGen provide the parameters for this structure? Is there another way to do this. I can't attach the pdb file to this email because the editor doesn't support it.

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version: Gromacs 2016
Method: plain MD sampling of ligand (mol attached) coordinated to Mg in a solvent box.

Expected Behavior

Actual Behavior

I ran a quick simulation of the ligand attached (TPP.mol), which contains a diphosphate tail and is coordinated to Mg (the ion parameters used were from the OPLS-AA/M force field for Gromacs). I noticed that very quickly the phosphate group gets distorted ("example.pdb" attached; for a comparison I also attached the starting structure "starting.pdb").

I wonder whether it is a force field or a file conversion issue? I noticed for instance that in the Gromacs topology file (ligand.itp) there are a number of torsions with all force constants set to zero.

files.zip

Hello all,
Please, can you help to generate oplsaa parameters for attached structures?
Thanks
Mohammed

• This is a feature request

Dear LigParGen developers,

I want to simulate a large organic molecule (>200 atoms), but current version of LigParGen can only deal with molecules <= 200 atoms. I understand that this is because the QM calculation for large molecules is time-consuming. To address this issue, is it possible to provide an interface, such that I can submit an output of calculation by a QM software (for instance, Orca), to generate OPLS parameters for large molecules?

Thanks,
Haohao

Dear Leela
Thank you for the support.
I have tried to generate oplsaa parameters for the new structures using the web site but didn't work and the error is unknown.
All of the molecules have zero net charge and they are canonicalised.
Please, can you help by generating oplsaa parameters for the attached structures?
Thanks

Mohammed structures.tar.gz

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :
Method:

Expected Behavior

Actual Behavior

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

This is an issue with the ligpargen web interface.

Expected Behavior

Some warning or error when both a smiles string and file are selected for upload. This can happen if a user hits the back button after submitting a file, then puts in a smiles string ie,
file upload -> generate -> back button -> smiles -> generate

Actual Behavior

The selected file is cleared on hitting the back button in a browser or some sort of warning/error if a user manages to have both a file uploaded and a smiles string.

This is pretty nit-picky but something I noticed when I was generating OPLS parameters using smiles and pdb files and using the back button. It does use the most recent user input so its not too bad, but I was a bit confused when I was trying to remember what I used to generate some OPLS parameters and saw both a file uploaded and a smiles string.

I believe this to be a bug with LigParGen

Issue Information

Software name & Version : LigParGen server from website
Method: I am a first time user of this server, so tested alanine to check if generated partial charges for the residue (after redistributing charges) are consistent with current aminoacid.rtp file for OPLS-AA/M

Observation

Would you tell me please how can I obtain gro and topology file for copolymer : PEO-PS contains 2 residues?

I submit PEO (100monomer) Found residue ligand OXY
Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code.

• [x ] I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version : LigParGen

Expected Behavior

Entered the SMILES of HCN,CN- or HCCH into LigParGen to receive topology and parameters. Example of SMILES: C#N for HCN.

Actual Behavior

Instead of a successful generation of topology files, I received the error message 'Problem found in the file format. Please, check the input file. In case you are not able to find the error we suggests to use the SMILE code'.

I only receive the error for linear molecules out of the ones I have tested. Is there any way to automatically generate files for these linear molecules?

Kind regards,

Hilda

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• This is a feature request

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Expected Behavior

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• I believe this to be a bug with LigParGen
• This is a feature request

I am having some issues with LigParGen being able to read in mol files for a molecule I am trying to parameterise (thiamine diphosphate, net charge of -2).

I generated mol files using a few different programs (attached) from a mol2 file initially made with Maestro (TPP.mol2). When trying to run LigParGen with any of these mol files, I get the error “Found residue ligand UNK. Unknown error. Please check input file.”. The problem might be with reading in the file: if I use the chemical drawer on the website, and paste the same mol file in there (the molecule gets uploaded correctly), then make SMILES from it and run the program, all goes fine and the molecule is indeed parameterised. On the other hand, if I build a test molecule in Maestro (e.g. benzene) and upload its mol file, all goes smoothly, so it doesn’t seem to be a general issue with the mol format written by Maestro.

mol_files.zip

I am using LigParGen Server for generating OPLS-AA Force Field parameters for small organic molecules. I have doubt regarding dihedral parameters. I am taking parameters from .key file. Energy expression for dihedral are:
E (dihedrals) = V1 / 2 (1+cos(phi)) + V2 / 2 (1-cos(2phi)) + V3 / 2 (1+cos(3phi)) + V4 / 2 (1-cos(4*phi))

The parameters reported in .key file are for V1, V2, V3 or for (V1/2), (V2/2), (V3/2).

Thanks,
Anand

Hi Leela,
I was trying to generate parameters for acetonitrile with smile code ("CC#N") and as well as with PDB. But getting error. While I tried the same thing for propionitrile ("CCC#N"), it is giving perfect result. Please help me.

Thanks & regards,
Pranab.

LigParGen has some issues generating parameters for molecules with C#N and C#C functional groups, because of a bond angle of 180 degrees and a dummy atom. We are trying to resolve this issue soon.

056.mol.txt

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#Hi, How reliable is this generator is. I tried for decane and it gives me different parameters for dihedrals. also can not found parameters for nitrate ion (NO3-)/.

Dear Developers,

I have tried to get the OPLS parameters for tannic acid, but it showed unknown errors. A couple of structures optimized with semi-empirical methods were tested. The molecule has zero charge. Could you please help generate oplsaa parameters for the attached structure? I included several files for the same molecule. In addition, is the limit of 200 atoms still in play if I use command-line LigParGen. Thank you very much.

Best,
Xiao

tannic.zip

• I believe this to be a bug with LigParGen
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Expected Behavior

Actual Behavior

I believe this to be a bug with LigParGen

Issue Information

I generated parameters for the molecule attached to be used in Q6. I was surprised about the small Avdw value obtained for carbonyl . carbon 1059.1297 rather than 1802. I wonder the reason for such assignment.
In the itp gromacs file the same happens, the value does not correspond to the one observed for example in ASP.
Moreover, several torsions seems to be missing, which in reality exist for such group. Using ffld those parameters seems correct, but not with ffld

test-lig.zip

Many thanks in advance for your help

Fernanda Duarte
Associate Professor of Chemistry
Chemistry Research Laboratory
Mansfield Road
University of Oxford
Oxford OX1 3TA UK

• I believe this to be a bug with LigParGen
• This is a feature request

I wonder whether it is possible to allow molecules with net charge larger than +/-2 to be parameterised by the LigParGen Server?

• I believe this to be a bug with LigParGen
• This is a feature request

Found residue ligand UNK
Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code

Dear Leela,

I tried to generate the OPLS parameters for my model molecules several times but each time I face the error gate-way time out. The molecule sizes vary from 15 to 212 atoms but even for the 15 atoms
I get the same error. I will really appreciate if you could help to solve this problem. Here is the pdb file of the zero-charged and optimized molecules so I hope you could guide me to find out what is wrong.

Thanks in advance

I have 2 blocks copolymer :PEO-PS. When I submit the copolymer I have encountered with the

Found residue ligand UNK
Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code

How can I fix it?
Thank you

• I believe this to be a bug with LigParGen

Issue Information

Software name & Version : g
Method:

Expected Behavior

Actual Behavior

I have tried to use LigParGen which is online for generating topology parameters for my complex but always gives an error. I tried different complexes but no output.
Attached is the structure (MOL)

• I believe this to be a bug with LigParGen
• This is a feature request

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Method:

Expected Behavior

Actual Behavior

Using the web server on multicyclic molecules, the OpenMM .xml file contains some torsions that have all of the force constants = 0.00000.

A simple example is DABCO (smiles=C1CN2CCN1CC2) for which the output contains lines including:

Improper... class1="C807" class2="N802" class3="H819" class4="C806" k1="0.000000" k2="0.000000" k3="0.000000" k4="0.000000" ...

For some other molecules, both Proper and Improper torsions like this appear.

Are these non-functional torsions evidence of

1. a bug: there should be non-zero k's in there
2. torsions that should have parameters, but they just don't exist in OPLS-AA
3. torsions that resulted from a search, don't exist in OPLS-AA, aren't needed, and they can be deleted.
4. Something else?

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version : LAMMPS

Make LigParGen compatible for LAMMPS using CHARMM2LAMMPS conversion tool

• I believe this to be a bug with LigParGen
• This is a feature request

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Method:

Expected Behavior

Actual Behavior

• I believe this to be a bug with LigParGen
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Expected Behavior

Input File cordinates:

HETATM 5714 PG ANP A 601 -20.656 20.664 -48.770 1.00 58.40 P
ANISOU 5714 PG ANP A 601 9381 6930 5878 1478 76 639 P
HETATM 5715 O1G ANP A 601 -21.693 19.582 -49.260 1.00 57.20 O
ANISOU 5715 O1G ANP A 601 9430 6799 5503 1541 -86 573 O
HETATM 5716 O2G ANP A 601 -21.313 21.632 -47.730 1.00 57.55 O
ANISOU 5716 O2G ANP A 601 9068 6861 5935 1409 -106 553 O
HETATM 5717 O3G ANP A 601 -19.463 19.893 -48.106 1.00 56.48 O
ANISOU 5717 O3G ANP A 601 8940 6758 5762 1442 239 658 O

Output file cordinates :
1ANP H00 1 -1.974 2.510 -5.227
1ANP O01 2 -2.012 2.567 -5.294
1ANP C02 3 -2.117 2.641 -5.237
1ANP H03 4 -2.129 2.615 -5.131
1ANP C04 5 -2.239 2.615 -5.307
1ANP C05 6 -2.099 2.785 -5.252
1ANP H06 7 -2.219 2.599 -5.413
1ANP O07 8 -2.317 2.731 -5.289

my input file cordinates are in range from 20 to 30
and output gro cordinates are very much different and range in 1 - 10
because of which my ligand is placed somewhere else during simulation.

Actual Behavior

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :
Method:

Expected Behavior

Actual Behavior

Problem is with respect to the force field parameters of the lipid bilayer: dppc (Dipalmitoylphosphatidylcholine) molecule.

• I believe this to be a bug with LigParGen

Issue Information

Software name & Version : web service LigParGen

Expected Behavior

Force field parameters should be available

Actual Behavior

The opls-aa force field parameters are available when I keep the chain length of the dppc (Dipalmitoylphosphatidylcholine) molecule to
7 Carbon atoms, however, when I increase it to 14 the service shows error. It pointed me to post the error on this forum.
It would be great if the authors would fix this error. Also, I feel that the parameters for the alkyl chain CH2 groups won't really change so it shouldn't be a problem if I put 10 Carbon atoms or hundred.
Number of atoms in my molecule is 130 (less than the limit value of 200).

Regards,
Navya
IIT Guwahati
India

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Create BOSS2AMBER feature for server

Expected Behavior

Actual Behavior

• I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version :LigParGen
Method:LigParGen

Expected Behavior

Dear all
I'm to generate the parameters of nitrate. For that, I have created several .mol (even using the Draw molecule module here) as well as using the SMILE nomenclature without luck.

Actual Behavior

When using SMILES I'm getting the following error:
export BOSSdir=/var/www/html/ligpargen/apps/boss-4.9;/var/www/html/ligpargen/apps/anaconda2/bin/python2.7 /var/www/html/ligpargen/apps/ligpargenCode/Converter.py -s 'O=N(=O)[O-]' -r UNK -o 0 -c -1 > /tmp/errorServer.log
Problem found in the file format. Please, check the input file. In case you are not able to find the error we suggests to use the SMILE code

While, when using a mol file I'm getting the following error:
Found residue ligand UNK
Unknown error. Please, check the input file. If you are not able to find the error, we suggests to use the SMILE code

• I believe this to be a bug with LigParGen
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Hi Leela,

I was trying to get parameters for fluorinated carbons/thiols. LigParGen give correct parameters for LJ, bond, angles (consistent with previous paper by Watkins and Jorgensen, J. Phys. Chem. A 2001, 105, 4118-4125). The charges are different, which is fine because it is recalculated.
My question is:
Why dihedral potentials are so different? In fact, parameter for F-CF-CF-CF are 0, 0, 0, 0. Is it some issue of LigParGen?

UNK_849407.lmp.txt
UNK_849407.pdb.txt

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• [X ] I believe this to be a bug with LigParGen
• This is a feature request

Issue Information

Software name & Version : Gromacs 2018.7
Method:

Expected Behavior

I'm trying to generate a .itp and .gro file with simple tri-peptides with an electrophilic warhead attached

Actual Behavior

When the warhead contains an enone motif, The output file has carbon atoms completely out of place (usualy the CH3 on motif R-O-CO-CH-CH-CH3 )
I've tried different ways of generating my .mol file and inputing the SMILES code, but it doesn't work.