sybyl servers in umdnj
achilles.umdnj.edu are pretty fast due to users usually use apollo and titan.

MDL mol file format works fine on NCI, so I planed to download MDL mol file then convert to sybyl mol2 file format. (maybe use openbabel)
tested by using babel to convert it. it works this way.
I don't know why files generated by nci can't be read by sybyl, ex: pdb not work, sybyl mol2 not work. mol not work, should be convert by using babel.

when babel don't work, put the files in a dos8 directory, ex: use d:\temp instead of d:\program files\...

now, the only thing left is, how can I align those compounds by the core substructure automatically.