Hi Dong,

you can deal with your problems (too many pseudoatoms) in two ways: either explicitly defining all the pairs of atoms (or at least a few of them - you defined 291 independent pseudoatom) that you restraining, or using a modeller version suited for this particular problem. Since this morning you can find a modeller executable with 2000 possible pseudo atoms, on our ftp site:

ftp salilab.org

/pub/outgoing/mod_r10000

Andras