Subject: DISCO3 bonds across cell boundaries

From: [email-masked] (Mathias Brock)
Date: Fri, 16 Sep 1994 22:03:17 +0100 (DFT)

Dear netters,

considarable improvement by DISCOVER3 introducing bonds across
cell boundaries was found to cause problems.
The generated connectivity list is given below. The execution aborted
with error in bond geometry list between SI2 and O2 which information
was
-   SI2  O2%110#6
-   O2   SI2%11-1#6
 wonder, if these are is corrensponding atoms.
Shouldn't O2 be SI2%-1-10#6 or some similar.

Any suggestions ?...

M. Brock
[email-masked] 

---- start of MDF file ---
!BIOSYM molecular_data 4

!DATE:      Sat Jun 11 17:45:21 1994     INSIGHT generated molecular data file 

#topology                                                                      

@column 1 element                                                              
@column 2 atom_type cff91_czeo                                                  
@column 3 charge_group cff91_czeo                                               
@column 4 isotope                                                              
@column 5 formal_charge                                                        
@column 6 charge cff91_czeo                                                     
@column 7 switching_atom cff91_czeo                                             
@column 8 oop_flag cff91_czeo                                                  
@column 9 chirality_flag                                                       
@column 10 occupancy                                                           
@column 11 xray_temp_factor                                                    
@column 12 connections                                                         

@assembly MORSI4_CELL                                                         

@molecule MORSI4                                                              

SBD_Z0A:SI1         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O5%00-1 O1%00-1#6 O9%00-1#6 O10%00-1#6 
SBD_Z0A:SI2         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O6%001 O9#5 O2%110#6 O10%010#7 
SBD_Z0A:SI3         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O6%-1-10#5 O3%00-1#6 O8%00-1#6 O11%00-1#6 
SBD_Z0A:SI4         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O11%110#2 O5#5 O8#5 O4%110#6 
SBD_Z0A:SI5         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O12 O7 O1 O2%11-1#2 
SBD_Z0A:SI6         Si sz      SBD  0  4+  0.0000 0 0 8  1.0000  0.5000 O13 O7 O3 O4%11-1#2 
SBD_Z0A:O1          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI5 SI1#6 
SBD_Z0A:O2          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI5%110#2 SI2%11-1#6 
SBD_Z0A:O3          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI6 SI3#6 
SBD_Z0A:O4          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI6%110#2 SI4%11-1#6 
SBD_Z0A:O5          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI1%001 SI4%-1-10#5 
SBD_Z0A:O6          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI2%00-1 SI3#5 
SBD_Z0A:O7          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI6 SI5 
SBD_Z0A:O8          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI4%-1-10#5 SI3#6 
SBD_Z0A:O9          O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI2%-1-10#5 SI1#6 
SBD_Z0A:O10         O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI1#6 SI2%-11-1#7 
SBD_Z0A:O11         O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI4%11-1#2 SI3#6 
SBD_Z0A:O12         O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI5 SI5#4 
SBD_Z0A:O13         O  oss     SBD  0  2-  0.0000 0 0 8  1.0000  0.5000 SI6 SI6#4 

#symmetry                                                                       
@periodicity 3 XYZ
@group (CMC21) [ORIGIN_1]
!

#end