search

leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
20 stars 17 forks source link

Problem with phosphate ion and sulphate molecule #63

Open carlosdelacruz1 opened 4 years ago

carlosdelacruz1 commented 4 years ago

Nowadays there is no way to obtain the topology file for a common ion as the phosphate or sulphate. First the web page doesn't accept negative charge -3. And also if you try to run for the sulphate ion with charge -2 also gives error.

How can be possible that those common ligands present errors obtaining the topology file? For the sulphate I need to create the H2SO4 molecule and remove manually the protons and include manually the charges, so it's very tedious do it on that way.

Really is some one working in this issue or should I need to go to other forcefield

amani739861 commented 3 years ago

I compare the result of HNO3 like what you do with the paramters from the forcefield(https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm). It's quite different, and I believe this method is not valid. Did you find some other method to generate topology file of simple ions? or other friendly forcefield?

thanks