Timeline for How to convert a SMILES into a LAMMPS or GROMACS input file?
Current License: CC BY-SA 4.0
9 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Apr 21 at 20:29 | vote | accept | Pranoy Ray | ||
| Mar 11 at 12:03 | answer | added | Bdrs | timeline score: 3 | |
| Feb 29 at 1:49 | comment | added | Vladislav Gladkikh | @PranoyRay I mean avogadro software avogadro.cc can read SMILES string and convert to to an xyz file which contains x,y,z coordinates that you can put into your LAMMPS input file | |
| Feb 25 at 15:35 | comment | added | Roshan Shrestha | @PranoyRay For charmm, you need to look into its database since it's not automated like the ligpargen server. | |
| Feb 23 at 21:42 | comment | added | Pranoy Ray | @VladislavGladkikh what do you mean? please elucidate your comment | |
| Feb 23 at 21:40 | comment | added | Pranoy Ray | @RoshanShrestha what if I want to build CHARMM parameters? | |
| Jan 30 at 2:49 | comment | added | Vladislav Gladkikh | Does it have to be python? Can you open it in avogadro and then save as an xyz file? | |
| Jan 25 at 6:42 | comment | added | Roshan Shrestha | Have you looked into github.com/Isra3l/ligpargen ? It builds OPLS -AA parameters from the smiles. | |
| Jan 25 at 1:04 | history | asked | Pranoy Ray | CC BY-SA 4.0 |