AMBER Archive (2002)

Subject: How to decrease the solvated system in Amber6?

From: Ling Zhang (lz267_at_nyu.edu)
Date: Mon Jul 01 2002 - 11:28:51 CDT

Dear all,

I tried to decrease my solvated system by using a trucated octahedral
box in Leap of Amber6. But the result is still not satifactory. Could
you give me some suggestions in decreaseing the system without
affecting the quality of the simulation? Thanks a lot.

By the way, I used the simulaid.bin programe to find optimal position
of solute. If someone has experince in using this programe, could you
tell me how to set the smallest image-image distance before optimizing
the orientation of solute in a trucated octahedron? I have a system of
more than 900 protein residues and almost 350 crystal waters. Thanks
again.

Best,
Ling