VMD-L Mailing List
From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Sep 26 2016 - 21:46:54 CDT
By using the "solvate" and the "Add Ions" plugins in vmd, we will get the pdb files with the protein solvated in water and supplemented with ions. However, both of these two plugins change the chain identifiers of the original pdb file. For example, in the original pdb file, the chains of the protein and named as A, B, C,... (the fifth column of the original pdb files) , but in the pdb files generated by the "solvate" and the "Add Ions" plugins, the original chain identifiers "A", "B", "C",... all turn into "P" (the fifth column of the newly generated pdb files). My question is whether there is a way to keep these chain identifiers unchanged when using these vmd plugins, and whether keeping them unchanged will affact the following NAMD simulation?