VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 27 2008 - 15:12:35 CDT

Hi,
  Niether the MSMS program nor Surf can really handle huge water boxes,
these are limitations of these two programs. The authors of those packages
never intended them to be used on structures of the size that you're
working with.

If you want to make a water box like the ones you've seen on our web site,
use the "volmap tool" plugin that's in the Extensions->Analysis menu.
You'll want to use "all" as the selection, and you'll want to adjust
the resolution down to something more like 2.0 or 3.0. Give that a try.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 27, 2008 at 03:53:54PM -0400, Yinglong Miao wrote:
> Dear VMDers,
>
> I have been trying to apply transparent surf or MSMS representation for
> water in a large system (2336817 atoms), but keep getting error messages as
> pasted below. I am wondering whether there is a size limit for these two
> representations. I did see nice images with these two presentations used for
> water in VMD gallery like:
> http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/Fig1-new2_st.jpg.html.
> How do you get around for large systems? Any help will be greatly
> appreciated.
>
> Thanks,
> Yinglong
>
>
> *Error messages for "surf":*
> vmd > Reading 2336817 atoms..done
> Probe radius = 1.400
> Constructing solvent-accessible surface ..
> Max edge length = 1.200
> Malloc of zero or illegal length!!
> length = 0
> Malloc of zero or illegal length!!
> length = 0
> ..compute_tri_plane_int(): denom close to zero 0.000000
> compute_tri_plane_int(): denom close to zero 0.000000
> find_sol_cons() warning: sol is somewhat away from vertex (0.002365).
> .find_sol_cons() warning: sol is somewhat away from vertex (0.001152).
> ..find_sol_cons() warning: sol is somewhat away from vertex (0.001434).
> .compute_tri_plane_int(): denom close to zero 0.000000
> compute_tri_plane_int(): denom close to zero 0.000000
> find_sol_cons() warning: sol is somewhat away from vertex (0.003361).
> ...find_sol_cons() warning: sol is somewhat away from vertex (0.003765).
> ..find_ray_sphere_int(): disc = -0.042826 sqrt probs for atom center
> -128.998001
> -156.473999 3.010000
> Stop here
> Stop here
> Stop here
> Stop here
> ...
> Stop here
> Segmentation fault (core dumped)
> 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.
>
> *Error messages for "MSMS":*
> Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
> INPUT 2336817 spheres 0 collision only, radii 1.000 to 1.520
> PARAM Probe_radius 1.500 density 1.500 hdensity 0.000
> REDUCED SURFACE ...
> RS component 0 identified 71133 73188 93825
> 2 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 196596 294894 2 90806 3748
> Time Reduced Surface real: 9.15 user: 8.97 sys: 0.17
> ANALYTICAL SOLVENT EXCLUDED SURFACE...
> Component 0
> ERROR) No data from MSMS.. giving up.
> Info) Done with MSMS surface.
>
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078