VMD-L Mailing List

From: Dieter Blaas (dieter.blaas_at_univie.ac.at)
Date: Tue May 11 2004 - 08:13:20 CDT

When trying to render a surface of a virus with ~
350.000 coordinates I get the messages shown below,
then, after an awful lot of time an error message
appears saying something like "the program has made
an address exception....", the PC freezes and can only
be re-started with RESET. Win2k, 375 MB, HD free
space 11 GB:
Is there an upper limit for the number of coordinates to
be handled?
What can I do? Thanx for help, Dieter
.....................
vmd > Info) Using plugin pdb for structure file F:/all_60_
h2.pdb
Info) Using plugin pdb for coordinates from file
F:/Programme/F77/G77/bin/all_60
_h2.pdb
Info) Determining bond structure from distance search
...
Info) Analyzing structure ...
Info) Atoms: 362827
Info) Residues: 45360
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 180 Protein: 182 Nucleic: 0
Info) Finished with coordinate file
F:/Programme/F77/G77/bin/all_60_h2.pdb.
Reading 362827 atoms..done
Probe radius = 3.000
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
..............................find_sol_cons() warning: sol is
somewhat away from
 vertex (0.001048).
.......................................find_sol_cons() warning: sol is
somewhat
away from vertex (0.001038).
find_sol_cons() warning: sol is somewhat away from
vertex (0.001904).
...................find_sol_cons() warning: sol is somewhat
away from vertex (0.
003807).
.................find_sol_cons() warning: sol is somewhat
away from vertex (0.00
3555).
...............find_sol_cons() warning: sol is somewhat away
from vertex (0.0018
41).
........................find_sol_cons() warning: sol is somewhat
away from verte
x (0.001221).
........find_sol_cons() warning: sol is somewhat away
from vertex (0.002722).
...find_sol_cons() warning: sol is somewhat away from
vertex (0.004053).
.........find_sol_cons() warning: sol is somewhat away
from vertex (0.003754).
...find_sol_cons() warning: sol is somewhat away from
vertex (0.001486).
..........find_sol_cons() warning: sol is somewhat away
from vertex (0.002303).
..find_sol_cons() warning: sol is somewhat away from
vertex (0.001241).
..............find_sol_cons() warning: sol is somewhat away
from vertex (0.00230
0).
..find_sol_cons() warning: sol is somewhat away from
vertex (0.010190).
.....find_sol_cons() warning: sol is somewhat away from
vertex (0.001572).
..................find_sol_cons() warning: sol is somewhat
away from vertex (0.0
02974).
.