From: John Stone (
Date: Mon Oct 03 2016 - 16:10:19 CDT

  I think that this is likely a default behavior of psfgen, though for
what reason I'm not sure.

In principle it should trivial to collect the original chain names
from the original PDB file and re-apply them to the solvated or
ionized structure. This could be as simple as selecting atoms of each
chain type, querying their indices, and then using those indices to set
the chains in the newly generated structure and saving out another (3rd)
PDB file. NAMD generally shouldn't care about the chain
unless your own NAMD config files do something specific based on
chain information AFAIK.

  John Stone

On Tue, Sep 27, 2016 at 10:46:54AM +0800, sunyeping wrote:
> Dear all,
> 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?
> Best regards.
> Yeping Sun

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349