From: Chris Taylor (
Date: Wed Oct 06 2021 - 21:02:58 CDT


I changed the line in the script that says
set topologyfile [format "%s/plugins/noarch/tcl/membrane1.2/top_all27_prot_lipid.inp" $env(VMDDIR)]

And then I downloaded the example PDB and ran
vmd > source mergemultiframepdb.tcl
vmd > mol new Downloads/1k4r.pdb1 type pdb
Info) Using plugin pdb for structure file Downloads/1k4r.pdb1
Info) Using plugin pdb for coordinates from file Downloads/1k4r.pdb1
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 9084
vmd > Info) Finished with coordinate file Downloads/1k4r.pdb1.

That worked fine, but I keep getting errors like this and no file is written out. I tried with a couple of PDB assembly files I downloaded. Am I doing something wrong? I tried it on Windows 10 and Centos8, but I’m not sure that matters.

vmd > merge_multi_frame_structure top /home/cht/tmp Downloads/1k4r_merged.pdb
psfgen) Warning: failed to set coordinate for atom CD1 ILE:36 V6
PDB: /home/cht/tmp/merge0000.G.pdb V7
psfgen) building segment V7
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE
psfgen) reading residues from pdb file /home/cht/tmp/merge0000.G.pdb
psfgen) unknown residue type NAG
psfgen) unknown residue type NAG
psfgen) extracted 2 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown residue type NAG
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

From: Axel Kohlmeyer <>
Sent: Tuesday, October 5, 2021 21:43
To: Chris Taylor <>
Subject: Re: vmd-l: Merge frames of PDB asymmetric unit to biological assembly


This is not a plugin but just a script with some functions written in VMD/Tcl. And the script from the URL you quote will still work if you make a tiny adjustment (it works for me with the provided example): there is some location that points to the membrane plugin version 1.0. This plugin is in version 1.2 in my VMD installation, so I needed to edit the file accordingly. but other than that i just followed the instructions, downloaded the PDB file, uncompressed it. launched VMD, sources the tcl script. loaded the pdb file, then ran the command and then loaded the final pdb file. It is complaining about poorly guessed coordinates, but the atoms are still there.


On Tue, Oct 5, 2021 at 11:50 PM Chris Taylor <<>> wrote:
Hello, I ran across this old mailing list post:$>

It mentions using a plugin$> that doesn’t seem to be part of the distribution any more. The post describes something I’d like to do, for instance downloading the 5IRE “Biological Assembly 1” file from the protein databank and using the plugin to create a new structure with frames of trajectory 0-59 represented. Then, in VMD I could manipulate the icosahedral assembly as one structure. Is there an up to date way to do this? I was able to download an old version of the plugin from somewhere but I got lots of errors when I ran it. Thanks,

Dr. Axel Kohlmeyer<>;!!DZ3fjg!qAFuOa07DweNJNZYrW3gmzC6IceGY2awUY_0-h5RoFxz8L9dQ6t3ynPzF3TyaMmEQw$ <;!!LIr3w8kk_Xxm!47hwBdwdVFf8u8XVwBdGDqlkA_tnfVd0JjYWvzwhNYf0OKkizfB3fNAZgLp_jmY$>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.