use strict;

while (<DATA>) {
    print if (split ' ')[2] ne 'H';
}
__DATA__
ATOM 16 NZ LYS A 7 -19.664 15.558 -9.499  1.00 18.80 N
ATOM 17 H  LYS A 7 -19.967 21.014 -14.224 1.00 0.00  H