VMD-L Mailing List

From: Chris Taylor (christay_at_usc.edu)
Date: Tue Oct 12 2021 - 21:46:24 CDT

I’ve been working with this some more- I downloaded the 1k4r.pdb1 and 5ire.pdb1 biological assembly files from the RCSB.org protein databank and the mergemultiframepdb.tcl script. In VMD, I run

source mergemultiframepdb.tcl

.and then:
mol new 1k4r.pdb1 type pdb
merge_multi_frame_structure top /Users/cht/Downloads/temp 1k4r_merged

Sometimes this completes fine, and other times it dies with an error:

psfgen) reading coordinates from pdb file C:/Users/cht/Downloads/temp/merge0000.F.pdb for segment V6
psfgen) Warning: failed to set coordinate for atom CD1 ILE:36 V6
PDB: C:/Users/cht/Downloads/temp/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 C:/Users/cht/Downloads/temp/merge0000.G.pdb
psfgen) unknown residue type NAG
psfgen) unknown residue type NAG
psfgen) extracted 2 residues from pdb file
Info: generating structure...
psfgen) unknown residue type NAG

With another file, it seems to consistently error out and crash VMD when I run:

mol new 5ire.pdb1 type pdb
merge_multi_frame_structure top /Users/cht/Downloads/temp 5ire_merged

I get a similar error about the unknown residue type. I’ve tried on a Windows10 as well as a CentOS8 laptop, both with 16Gb RAM. It seems to have plenty of free RAM, not running any other apps. Has anybody else run into this?

Chris

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> On Behalf Of Chris Taylor
Sent: Wednesday, October 6, 2021 19:03
To: Axel Kohlmeyer <akohlmey_at_gmail.com>; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Merge frames of PDB asymmetric unit to biological assembly

Thanks-

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
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
“”

From: Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
Sent: Tuesday, October 5, 2021 21:43
To: Chris Taylor <christay_at_usc.edu<mailto:christay_at_usc.edu>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Merge frames of PDB asymmetric unit to biological assembly

Chris,

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.

Axel.

On Tue, Oct 5, 2021 at 11:50 PM Chris Taylor <christay_at_usc.edu<mailto:christay_at_usc.edu>> wrote:
Hello, I ran across this old mailing list post:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8118.html$>

It mentions using a plugin http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mergemultiframepdb/D6Q$> 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 RCSB.org 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,
Chris 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!v1NuBngCO5dVfUBCFGPXbHKVVp2nmzyVuxVZf3g5_MjJ7CeH5XjlZ6z0FEkO6UGPYw$ <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!LIr3w8kk_Xxm!47hwBdwdVFf8u8XVwBdGDqlkA_tnfVd0JjYWvzwhNYf0OKkizfB3fNAZgLp_jmY$>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.