From: Stefan Doerr (
Date: Tue Oct 04 2016 - 09:25:39 CDT

Hey Yeping,
if you want, you can give a look at the software I develop called HTMD
which works quite nice for building systems.
It's in python and I tested it and psfgen actually keeps the chain IDs.
As John said though, NAMD should not care about chains.

Here is an example how it looks to build a protein in CHARMM with HTMD

And the link to our webpage and tutorials:

If you have any questions feel free to ask.

On Tue, Sep 27, 2016 at 4:46 AM, 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