atoms forming bonds

please *always* copy the mailing list on your replies (gmail has an option
to make reply-to all default, btw)

When I visualize in VMD , they form auto-bonds. what can be the reason for

that is because VMD has no clue what your atoms represent and what units
you use. so it guesses and poorly so. you can tell VMD to not guess bonds
and it won't create them.