[Users-list] Problems with the Br visualisation by Gview from .kont files (Grid 22b)

[Branko]

Hallo,

Is anybody observed problem with Br- visualization in Gview. Briefly on 
the example of bromoazepame: the bromine atom cannot be visualized in 
appropriate way. Molecule is prepared by semi-empirical optimization in 
MOPAC (PM3 method), saved in mol2 format and used as impute. This means 
that bond length should be appropriate. Corresponding PDB file (made by 
GRIN) can be visualized without problem. Also .kont and .lont files 
“recognized” existence and position of the bromine atom (appropriately, 
I think), but visualization give the “cross” in the place were Br should 
be (black colored, as there is a C), without connectivity with the ring. 
After I am set the ring-Br distance on (unacceptable) shorter one (from 
1.89 to 1.75) and repeat the whole procedure, connectivity can be 
visualized, but the Br is 9again) assigned as C. Program options was set 
as follows: IHAC 0 or IHAC 1-the same problem exist; NPLA 3, MOVE 3, 
LIST –2, ALMD 0.5. Probes were water or the self-defined probe. A number 
of trials were done before writing this mail. Thank you in advance

Branko