From: Quynh Vo <quynhuvo28.gmail.com>
Date: Fri, 16 Aug 2019 20:13:52 -0400
Attachments available until Sep 15, 2019
Dear Amber users
Recently, I used the charm-gui to build a lipid bilayer membrane using Charmm36 force field to be simulated in AMBER. The system is having a hard time reaching equilibrium even after 100ns. I can give more details about the conditions I used to equilibrate the system at a later time.
For now, I traced back the steps and used chamber to convert the namd psf file myself. There are some substantial differences in the LJ A and B coefficients between the two parm output files. I attached the two files here: step5_charmm2amber.parm7 is from the charm-gui and prmtop is from chamber.
Do you know if this is due version mismatch between the chamber version I used (AmberTool19) and what was implemented in Charm-gui? If so, which file would be the most appropriate one to use?
