GROMACS version:gromacs-2023
GROMACS modification: No
Hi, I’m using gmx sasa to calculate the surface area for my martini models. I read the document and also checked the tutorial. I am still not clear about the format of vdwradii.dat file, what should be the atom name for the beads? Is it based on the force field or my topology file? Also what should I put under the ; " Masses for vsite construction" section?
Here are the log file of gmx sasa, my vdwradi.dat file and my pdb file which is consistent with the trajectory and the topology files i used.
last_frame.txt (67.5 KB)
Thank you so much if you could help!
log.txt (86.2 KB)
vdwradii.dat (11.5 KB)