leelasd ligpargen issues

leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen

http://traken.chem.yale.edu/ligpargen/

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issues

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Local Version of LigParGen lacks some Improper Dihedral parameters

#92 wutobias opened 2 years ago
1
ERROR IN LigParGen output: wrong atom partial charges - GLycerol molecule

#91 paolobotto opened 2 years ago
0
Issues with Glycerol data generated by ligpargen

#90 paolobotto opened 2 years ago
0
ANGfinal error using LigPargen executable

#89 arashelahi opened 2 years ago
0
Non-corresponding atom types in the molecule.xyz file with molecule.key file

#88 AlainWil closed 2 years ago
1
Error in generating OPLS-AA for deprotonated PFBS ( [F3C-(CF2)3-SO3]- )

#87 Smile098 opened 2 years ago
0
[BUG] Crash when submitting linear molecules

#86 chem-william opened 2 years ago
0
Fully halogenated molecules cannot be generated

#85 rcruzsilva opened 2 years ago
0
Question about van der Waals parameters for hydrogen atoms

#84 dimozino opened 2 years ago
0
Unable to generate topology for water

#83 ChiselledPeasant opened 2 years ago
1
Polyaromatics hydrocarbon molecule cannot been generated

#82 idmoncay opened 2 years ago
0
Request for LigParGen command line to stop using /tmp as the only (hardcoded) option for temporary files

#81 therealchrisneale opened 3 years ago
0
BOSSdir seems limited to 80 characters or fewer

#80 therealchrisneale opened 3 years ago
0
command-line only error: AssertionError: PROPOSED CHARGE IS NOT POSSIBLE: SOLUTE MAY BE AN OPEN SHELL

#79 therealchrisneale opened 3 years ago
0
Server Timing Out

#78 wilfonba opened 3 years ago
0
Unable to generate topology with graphene

#77 layzhaf opened 3 years ago
2
cannot submit my mol2 file.

#76 EwieM8 opened 3 years ago
0
Problem of installing LigParGen Server Locally

#75 sbkk000 opened 3 years ago
3
Problemst in creating itp file for acetonitrile(CH3CN)

#74 NaviChemist opened 3 years ago
2
Cannot generate ions

#73 marcodigennaro opened 3 years ago
2
itp file generation with BOSS executable, using pdb files

#72 arashelahi opened 3 years ago
0
Issue of improper dihedral angles: atom indices are shuffled

#71 kobaya-sh opened 3 years ago
0
Unexpected torsions assigned for cyano group

#70 djcole56 opened 3 years ago
0
Issues related to input file format and No Output

#69 dalipntu opened 3 years ago
0
The index of atoms of my molecules are rearranged

#68 wwww0wwww opened 3 years ago
0
I can' t get the opls-aa parameter for this smil character

#67 ExuanW opened 3 years ago
0
Error when generating topology for Chloride anion

#66 Usmanovsky opened 3 years ago
0
The online server does not work

#65 ALANLI0258 opened 3 years ago
2
Force field for H+ and OH-

#64 mj-rezayani opened 3 years ago
0
Problem with phosphate ion and sulphate molecule

#63 carlosdelacruz1 opened 3 years ago
1
The atomtype opls_800 not found.

#62 drrahulsuresh opened 3 years ago
1
networks version causing 'node' attribute error

#61 punkpony opened 4 years ago
1
command line is always looking for .mol, independent of options and crashes if not found

#60 punkpony opened 4 years ago
2
LigParGen Parameterized Ligand Introduces Non-zero Charge to The System

#59 MikeBie opened 4 years ago
1
Invalid Order for Atomtypes in The Server Generated .itp File

#58 MikeBie opened 4 years ago
1
Issue Generating Topology Files for Saccharinate Anion

#57 peiyinlee opened 4 years ago
0
Hi

#56 sajjad-ah opened 4 years ago
1
Problem with SO42-

#55 carlosImdea opened 4 years ago
0
Error in generating topology of a ionic liquid anion

#54 Satyam2101 opened 4 years ago
1
Unable to get FF parameters for IT-4Cl (C94H78Cl4N4O2S4)

#53 Yuta-Yoshimoto opened 4 years ago
3
Angles in ketones not adding up to 360°

#52 marvinbernhardt opened 4 years ago
0
Bug Reading .pdb Files?

#51 Bohrealis opened 4 years ago
0
Problem generating .gro and .itp files with enones

#50 LeoFHall opened 4 years ago
0
Ligpargen produces Torsions with all k=0.00000 in OpenMM .xml file

#49 bkpgh opened 4 years ago
0
Atom numbering

#48 bkpgh closed 4 years ago
0
AssertionError: Hydrogens are not added. Please add Hydrogens

#47 calvanid opened 4 years ago
0
requesting meaningful OPLSAA atom types in output files

#46 jewettaij opened 4 years ago
10
Unable to generate .top and .rtf files for BNZ.pdb file

#45 draskot opened 4 years ago
0
OPLS-AA/M ff parameters for Alanine - inconsistent

#44 Neenz231 opened 4 years ago
2
I am not getting topology file for my compound with below smiles format O(Cc1n(CCCCCCCCCCCCCCCC)nnc1)c1c(Cc2c(OCc3n(CCCCCCCCCCCCCCCC)nnc3)c(-n3nc4c(n3)cccc4)cc(C(CC(C)(C)C)(C)C)c2)cc(C(CC(C)(C)C)(C)C)cc1-n1nc2c(n1)cccc2

#43 Muneeb-Aliyarhussain opened 5 years ago
0