TMD: initial and targeted structure does not have same number of atoms

From: Rabeta Yeasmin (
Date: Tue Mar 07 2017 - 09:42:58 CST


I am trying to set up a TMD simulation of a protein-lipid system. In the
targeted structure, the protein is inside the lipid while protein is
outside the lipid in the initial structure. I have tried to set up initial
structure using charmm-gui (the program used to set up the targeted
structure). But it looks like the total number of atoms is different in the
targeted and initial(charmm-gui) structure. It may due to different number
of water molecules in the two structure.
How can I set up the initial structure having same number of molecules as
the targeted structure?
Can anyone please help me with this?

Thank you.

Rabeta Yeasmin

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:09 CST