Frank V. Marcoline

Dear Nicolás Espinoza, We suggest the following two step process, which assumes linearity holds: 1) Perform a normal solvation calculation in the absence of a membrane potential. 2) Perform a calculation similar to the way apbsmem performs gating charge calculations: a) Create a copy of your protein with all of the charges set to zero. apbsmem can do this for you: java -cp <path_to_apbsmem>/apbsmem.jar apbsmem.ChargesOff input.pqr neutral.pqr b) Perform a dummy solvation calculation with the neutral...

Hi Adrián, You can still run APBSmem from the command line. Command line syntax: java -jar apbsmem.jar [inputfile [outputdiectory]] If you specify both the input file and output directory, the gui will still pop up, but APBSmem will run and exit when done. If the gui is an issue (for instance, if you are running on a machine without a display device) it is more complex, but still doable: 1) Run APBSmem, set up the calculation, and run it once to generate two input files: a .dummy.in file and a .solv.in...