[gmx-users] loop simulation

[egorov]

Dear gmx-users,
please, help me in the next question.

System:
Protein with bound cofactor. Both structures - with bound
cofactor and without it are known cristallographically. There is a
loop without organized second structure in the bining pocket. This
loop is situated very close to protein core when without cofactor and sligtly
away the core when cofactor is bound. By its outer side this loop take
part in ligand binding, but by inner - close cavity between itself and
protein core.

Question : could I and if so, then how to use MD to produce
relatively well-grounded structure with bound cofactor and opened cavity.

Best regards,
D.Egorov
Department of Clinical Laboratory and Microbiological Diagnostics,
Ural State Meical Academy mailto:egorov at newhospital.ru
12.04.2004.