GROMACS version: 2018
GROMACS modification: Yes/No
My MD studies are based on CHARMM force field. I want to generate topology parameter file for a molecule using ATB server. How can I select the files that suites for the all atom force field CHARMM.
I uploaded the PDB file of the molecule and as mentioned in protein data bank for the net charge of the molecule, the value was given to the ATB server. And as the output, three cases were shown with different RMSDs. How can I select the correct itp file that is suitable for CHARMM force field? And what are these results with different RMSDs indicates?
ATB is for the GROMOS force field. Do not try to use any topology it generates with CHARMM.
If you need a CHARMM topology for some species, use the CGenFF server or set the system up with CHARMM-GUI (which interfaces with CGenFF for ligands and other arbitrary species).