VMD-L Mailing List

From: Ezequiel Quintana Morales (ezequiel_at_ipna.csic.es)
Date: Tue Oct 16 2007 - 07:33:07 CDT

Hi,

I'm trying to draw a MSMS surface of a set of small organic molecules
I'm working with and I'm seen what it seems to me a strange behaviour of
MSMS.

I'm using VMD 1.8.6 (x86_64) and MSMS (x86_64) from inside VMD.

In short, the problem is: I can draw a msms surface of several atoms of
the whole set of molecules when i select 'Which Atoms: Selected and
Probe Radius: 1.5' but the surface disappears when I change 'Which
Atoms: All and Probe Radius: 1.5'. The surface is visible again when
'Which Atoms: All and Probe Radius: 2.0'. Of course, the group of atoms
and not buried and they are in a inner open surface.

I think that if I'm able to obtain the surface with a probe radius of
2.0, at a value of 1.5 should make it also be visible ...

Any help will be appreciated

Thanks
Ezequiel

PS. This is the output of MSMS for each calculation:

Surface obtained using 'Which Atoms: Selected'
                       'Sample Density: 12.6'
                       'Probe Radius: 1.5'

Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
1357 &'
INPUT 72 spheres 0 collision only, radii 1.000 to 1.500
PARAM Probe_radius 1.500 density 12.600 hdensity 0.000
REDUCED SURFACE ...
    RS component 0 identified 9 65 6
    0 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 200 300 0 72 15
    Time Reduced Surface real: 0.00 user: 0.00 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component 0
        Time Surface real: 0.01 user: 0.00 sys: 0.00
ordonne_arete: warning hole in a reentrant face 233
        Time Singularities real: 0.00 user: 0.00 sys: 0.00
    SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
         0 622 1269 41 644 38 1 0 3
TRIANGULATION...
    Component 0
    component#, vertices, edges, faces, genus, density
        0 10116 30360 20240 3 0.000
        Time Triangulation real: 0.09 user: 0.09 sys: 0.00
MSMS terminated normally
Total Time real: 0.12 user: 0.10 sys: 0.00
MSMS END
Info) Done with MSMS surface.
Info) Performing ACTC Triangle Consolidation...
Info) ACTC: Created 2634 triangle strips
Info) ACTC: Average vertices per strip = 9

No surface obtained using switching to 'Which Atoms: All'
with the same 'Sample Density: 12.6' and 'Probe Radius: 1.5'

Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
1361 &'
INPUT 510 spheres 438 collision only, radii 1.000 to 1.900
PARAM Probe_radius 1.500 density 12.600 hdensity 0.000
REDUCED SURFACE ...
    RS component 0 identified 14 12 13
    0 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 750 1125 0 338 19.5
    Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component 0
        Time Surface real: 0.00 user: 0.01 sys: 0.00
ERROR) No data from MSMS.. giving up.
Info) Done with MSMS surface.

Surface obtained again using 'Which Atoms: All'and 'Sample Density:
12.6'
but switching to 'Probe Radius: 2.0'

Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
1364 &'
INPUT 510 spheres 438 collision only, radii 1.000 to 1.900
PARAM Probe_radius 2.000 density 12.600 hdensity 0.000
REDUCED SURFACE ...
    RS component 0 identified 14 12 7
    0 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 686 1029 0 310 17.5
    Time Reduced Surface real: 0.05 user: 0.04 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component 0
        Time Surface real: 0.00 user: 0.01 sys: 0.00
ordonne_aretes: No cycle in face 61 (nba=-3)
ordonne_aretes: No cycle in face 64 (nba=-3)
ordonne_aretes: No cycle in face 570 (nba=-2)
ordonne_aretes: No cycle in face 571 (nba=-3)
 4 faces with problems
radius of atom 30 goes from 1.500000 to 1.600000
radius of atom 31 goes from 1.000000 to 1.100000
radius of atom 112 goes from 1.500000 to 1.600000
radius of atom 113 goes from 1.000000 to 1.100000
radius of atom 121 goes from 1.000000 to 1.100000
Failed to compute level 0 surface, try again 2
REDUCED SURFACE ...
    RS component 0 identified 14 12 7
    0 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 686m 1029 0 310 17.5
    Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
    Component 0
        Time Surface real: 0.00 user: 0.00 sys: 0.00
        Time Singularities real: 0.01 user: 0.00 sys: 0.00
    SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
         0 568 1230 52 662 74 0 0 1
TRIANGULATION...
    Component 0
    component#, vertices, edges, faces, genus, density
        0 6818 19882 13255 -94.5 0.000
WARNING: Genus mismatch (ana = 1.0, tri = -94.5 )
        Time Triangulation real: 0.09 user: 0.09 sys: 0.00
MSMS terminated normally
Total Time real: 0.21 user: 0.20 sys: 0.00
MSMS END
Info) Done with MSMS surface.
Info) Performing ACTC Triangle Consolidation...
Info) ACTC: Created 1860 triangle strips
Info) ACTC: Average vertices per strip = 9