From: Parker de Waal (
Date: Tue Sep 23 2014 - 20:27:08 CDT

Hello everyone,

Iíve recently been working with membrane protein simulations, generated by the CHARMM-GUI membrane builder and simulated in AMBER, and am trying to figure out a way to trim down on excess system padding (resulting from the unoptimized GUI).

What I would like to do is be able to take the generated protein/membrane PDB, select a rectangular region with origin x,y,z and dimensions a,b,c, and then delete everything else that doesnít fall within that selection. This way I can reduce my atom count and help get more ns/day for the simulation.

Does anyone know if this is possible in VMD, or perhaps another tool?