Package Details: vmd 1.9.4a38-3

Git Clone URL: (read-only, click to copy)
Package Base: vmd
Description: Visual Molecular Dynamics
Upstream URL:
Licenses: custom
Conflicts: vmd-src
Provides: vmd
Submitter: rata
Maintainer: berquist
Last Packager: berquist
Votes: 20
Popularity: 0.87
First Submitted: 2006-07-10 06:25
Last Updated: 2019-12-19 04:28

Latest Comments

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pmadhikar commented on 2020-07-14 13:16

Hi @berquist, thanks for this package!

I just wanted to let you know that vmd 1.9.4a38 is no longer available from the VMD website (at least I couldn't find it). It looks like they updated it on 29/05/2020 to 1.9.4a43.

I managed to tweak this package and have it install for me successfully, but I thought I ought to let you know. The new archive file is called vmd-1.9.4a43.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz

I installed it by editing the archive name in this package and updating the checksum.

Please update this package when you can.

a.kudelin commented on 2020-03-16 16:29

@David01, have you installed the package?

David01 commented on 2020-02-27 11:04

@dviktor Ok, thanks. I did that, no errors in building (see below, "Building process"). I cannot find the executable to run the program, the most similar is this:

[david@david-pc ~/programs/vmd]$ ./pkg/vmd/usr/bin/vmd
/usr/lib/vmd/vmd_LINUX: Command not found.

Building process:

[david@david-pc ~/programs/vmd]$ ls
PKGBUILD                                                                 vmd.desktop  vmd.png
vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz  vmd.install
[david@david-pc ~/programs/vmd]$ makepkg
==> Making package: vmd 1.9.4a38-3 (2020-02-27T11:54:58 CET)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
  -> Found vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz
  -> Found vmd.desktop
  -> Found vmd.install
  -> Found vmd.png
==> Validating source files with sha256sums...
    vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz ... Passed
    vmd.desktop ... Passed
    vmd.install ... Passed
    vmd.png ... Passed
==> Extracting sources...
  -> Extracting vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz with bsdtar
==> Entering fakeroot environment...
==> Starting package()...
Make sure /home/david/programs/vmd/pkg/vmd/usr/bin/vmd is in your path.
VMD installation complete.  Enjoy!
==> Tidying install...
  -> Removing libtool files...
  -> Purging unwanted files...
  -> Removing static library files...
  -> Stripping unneeded symbols from binaries and libraries...
  -> Compressing man and info pages...
==> Checking for packaging issues...
==> Creating package "vmd"...
  -> Generating .PKGINFO file...
  -> Generating .BUILDINFO file...
  -> Adding install file...
  -> Generating .MTREE file...
  -> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: vmd 1.9.4a38-3 (2020-02-27T11:57:17 CET)

dviktor commented on 2020-02-27 10:49

@David01 unpack snapshot and move vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz to the unpacked directory where PKGBUILD resides. Then run makepkg

David01 commented on 2020-02-27 10:47

@dviktor Thanks, I've downloaded vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz from the VMD site. Additionally, I've Downloaded snapshot from this site, which gives a vmd.tar.gz file. I extract it, this gives a vmd folder. I have copied the vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz to the vmd folder. How could I now perform the installation? Many thanks for your help

dviktor commented on 2020-02-27 09:49

@David01 you should manually download this package from VMD site and place it with PKGBUILD together

David01 commented on 2020-02-27 09:47

Thank you for maintaining this useful package.

I've tried to install it, but I receive the following error:

Could you please help me ?

Many thanks

[david@david-pc ~]$ yay -S vmd
:: Checking for conflicts...
:: Checking for inner conflicts...
[Aur: 1]  vmd-1.9.4a38-3

  1 vmd                                      (Build Files Exist)
==> Packages to cleanBuild?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> a
:: Deleting (1/1): /home/david/.cache/yay/vmd
:: Downloaded PKGBUILD (1/1): vmd
  1 vmd                                      (Build Files Exist)
==> Diffs to show?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==> n
:: Parsing SRCINFO (1/1): vmd
==> Making package: vmd 1.9.4a38-3 (2020-02-27T10:44:13 CET)
==> Retrieving sources...
==> ERROR: vmd-1.9.4a38.bin.LINUXAMD64-CUDA10-OptiX600-RTX-OSPRay170.opengl.tar.gz was not found in the build directory and is not a URL.
Error downloading sources: vmd

alexispaz commented on 2020-02-12 18:58

Could you please add the installation command for the other binaries distributed by vmd (e.g. catdcd)? May be using a wrapper? I would suggest something like:

diff --git a/PKGBUILD b/PKGBUILD
index a99be59..d17f479 100644
@@ -42,4 +42,9 @@ package() {

   install -Dm644 ${srcdir}/vmd.desktop ${pkgdir}/usr/share/applications/vmd.desktop
   install -Dm644 ${srcdir}/vmd.png ${pkgdir}/usr/share/icons/hicolor/512x512/apps/vmd.png
+  # Install wrapers to avoid install the libraries
+  mkdir -p ${pkgdir}/usr/bin
+  install -Dm755 ${srcdir}/catdcd ${pkgdir}/usr/bin/catdcd
diff --git a/catdcd b/catdcd
new file mode 100644
index 0000000..fbf32b6
--- /dev/null
+++ b/catdcd
@@ -0,0 +1,6 @@
+export LD_LIBRARY_PATH="/usr/lib/vmd:$LD_LIBRARY_PATH"
+/usr/lib/vmd/plugins/LINUXAMD64/bin/catdcd5.1/catdcd $@
+exit 0 

dviktor commented on 2019-12-19 14:48

@E3LDDfrK there is a request because it is pre-built version from developers. They are also providing source code for users to build it by themselves

hsayniaj79 commented on 2019-12-18 14:32

The sha256 sum of vmd.desktop is 942b752e2c9c1d6e3adb55ccdee14d1794640c341ddb7d8d70fb02396dafe81a A small edit in the PKGBUILD will fix the error.