VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Oct 10 2016 - 21:04:45 CDT

Thank you for the reply. But even if the chain IDs are kept during the system building up, the chain IDs are also changed in dcd output by NAMD. If you extract PDB files from the NAMD dcd trajectory, you will see all the chain IDs are "P" even they are defferenct in the initial input PDB files. This will lead to visualization problems in some software such as pymol.
Best regards.   ------------------------------------------------------------------From:Stefan Doerr <stefdoerr_at_gmail.com>Time:2016 Oct 5 (Wed) 15:00To:孙业平 <sunyeping_at_aliyun.com>Cc:vmd-l <vmd-l_at_ks.uiuc.edu>Subject:Re: vmd-l: chain identifier change in the pdb files generated by the "solvate" and "Add Ions" plugin
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
https://gist.github.com/stefdoerr/28b7a1cced1ad2dade640f6101eef258

And the link to our webpage and tutorials:
www.htmd.org

If you have any questions feel free to ask.

On Tue, Sep 27, 2016 at 4:46 AM, sunyeping <sunyeping_at_aliyun.com> 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