Create ligand topology file with OPLS force field

User discussions
1

Dear all

I was trying to get the OPLS-AA parameters for my ligand from LigParGen using PDB.

In case of PDB I found the error: " Found residue ligand UNN".

In case of smles code, I encountered the error, "Sorry, an error has been detected in your input data (file, smile or selected charge): 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 ‘C1=C(C=C(C(=C1O)O)O)C(=O)OC2=CC(=CC(=C2O)O)C(=O)OCC3C(C(C(C(O3)OC(=O)C4=CC(=C(C(=C4)OC(=O)C5=CC(=C(C(=C5)O)O)O)O)O)OC(=O)C6=CC(=C(C(=C6)OC(=O)C7=CC(=C(C(=C7)O)O)O)O)O)OC(=O)C8=CC(=C(C(=C8)OC(=O)C9=CC(=C(C(=C9)O)O)O)O)O)OC(=O)C1=CC(=C(C(=C1)OC(=O)C1=CC(=C(C(=C1)O)O)O)O)O’ -r UNK -o 0 -l -c 0 > /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.

I would be happy to know your opinions and get your advice.

2

I couldn’t get it to work with ligpargen either, would you be able to use a different forcefield? I tried converting the SMILE code to a pdb file using openbabel (set to generate 3D coordinates and add missing hydrogens) and when searching the file on ATB, it seems some matching topologies already exist on that server.

I also got it to work for the CgenFF server by using avogadro to convert the pdb to a mol2 file and uploading that

3

Thank you for your valuable advice @Karis
I also used CHARMM and prepared my ligand topology via SWISSPARAM