VMD-L Mailing List

From: Dmitry Suplatov (genesup_at_gmail.com)
Date: Thu Apr 11 2024 - 08:04:45 CDT

Hello,

I am having problems with ‘Surf’ as a “Drawing method” for proteins in VMD.

So, I installed VMD 1.9.3 from this package -
vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz. However,
with VMD 1.9.4a I have the same problem.

I used a default sequence of commands to deploy the package. However, it is
important to note that I *installed it to my local folder*, not the global
one.

tar xzf vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz
cd vmd-1.9.3/
mcedit configure
-> # Set these variables at the top of the script:
-> #$install_bin_dir="$ENV{'HOME'}/vmd/bin";
-> #$install_library_dir="$ENV{'HOME'}/vmd/lib/$install_name";
./configure
cd src/
make install
export PATH=$HOME/vmd/bin/:$PATH

Now I can run VMD using the ‘vmd’ command. When I load a pdb file and
select ‘Surf’ as the ‘Drawing method’ the following happens - the 3D-viewer
remains absolutely empty, I see this output in the bash command line of
Linux, from which the vmd was launched:

vmd > Reading 6882 atoms..done

Probe radius = 1.400

Constructing solvent-accessible surface ..

Info) This surface is made with SURF from UNC-Chapel Hill. The reference
is:

Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable Computation

Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,

Info) v. 14 (1994) pp. 19-25.

Info) Reading Surf geometry output file...

Info) Read Surf output file, processing geometry...

Info) Done.

The next immediate action that I did was to investigate if the ‘surf’
binary is correctly installed and set. So, while VMD was still running, I
located the ‘surf_LINUXAMD64’ binary and renamed it:

mv lib/vmd/surf_LINUXAMD64 lib/vmd/surf_LINUXAMD64_bak

Then, I again selected ‘Surf’ as the ‘Drawing method’, and saw the
following in the command line:

vmd > sh: line 1: [my home folder]/vmd/lib/vmd/surf_LINUXAMD64: No such
file or directory

ERROR) Cannot read SURF output file: /tmp/vmdsurf.u1713953541.664.in.tri

Info) Done.

So, this tells me that the ‘surf’ binary exists and VMD is recognizing it
(i.e. it throws an error when such binary is renamed, and no error when its
in place). But for unknown reason the ‘Surf’ representation still does not
work.

*Questions:*

   1. *Did anyone experience this and knows how to solve this?*
   2. *Perhaps, the problem is with the temporary folder that is used to
   exchange data between VMD and Surf binary. Is there any way to set this
   folder from /tmp to a specific location?*

Thanks and all have a great day

Dmitry