VMD-L Mailing List

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Tue May 27 2008 - 14:53:54 CDT

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