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leelasd
A repository for tutorials and FAQ's about LigParGen
Dear all, I have a small question rather related to opls than to ligpargen. I have noticed that for all elements, except for hydrogens, opls and amber vdw parameters are...
- [ ] I believe this to be a bug with LigParGen ## Issue Information Software name & Version : Method: Not sure what to write here, since my problem...
**Issue Information** Software name & Version : Gromacs-2020.2 Method: oplsaam.ff forefield; command: gmx grompp -f ions.mdp -c input.gro -p topol.top -o ions.tpr Note: _NOTE 2 [file topol.top, line 55]: System...
Good morning! Unfortanutelly, I am not able to create itp and gro file for acetonitrile. I used several variants for that, using pdb file, smile code created in draw molecula...
I have tried to generate LAMMPS data file for a polyaromatic hydrocarbon structure, however, it has not been possible. PDB file of the molecular structure can be accessed by following...
- - [ ] I believe this to be a bug with LigParGen - [ ] This is a feature request ## Issue Information Software name & Version : Method:...
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=S(=O)([N-]S(=O)(=O)C(F)(F)F)C(F)(F)F' -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...
This is a feature request ## Issue Information $ LigParGen -h usage: LigParGen [-h] [-r RESNAME] [-s SMILES] [-m MOL] [-p PDB] [-o {0,1,2,3}] [-c {0,-1,1,-2,2}] [-l] Ligand Parameter Generator...
- This is a feature request to allow BOSSdir to be longer than 80 characters. Not sure if the issue is in BOSS or LigParGen (command-line version) ## Issue Information...
- I believe this to be either a bug with LigParGen (command-line version only), or perhaps the online webserver is doing additional preparatory steps that I have not included for...