AMBER Archive (2002)

Subject: Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation)

From: Wu, JianHui(IAF)(LAVAL) (JianHui.wu_at_inrs-iaf.Uquebec.ca)
Date: Thu Mar 28 2002 - 11:56:04 CST

Dear Amber users,

The questions are related to Amber 6.0.
(1)
While trying to run MD with GB (igb=1 gbsa=1)on a protein of 250 residues,
Sander stop with error message 'Memory not enough, increase MATOM in
nmr.h'. The message is clear enough but it seems nmr.h is related to nmr
refinement and I never try to use nmr restraint here. Do I have other choice
other than increase MATOM and re-compile Sander? Say, switch off the nmr
refinement module somewhere?
(2)
Some single-point mutation would bring large conformational change. I can
not afford explicit water simulation and GB or GB/SA in amber 6.0 become my
choice. Perhaps a couple ns MD simulation with GB or GB/SA is good enough to
address the issue? I am sure a lot of other amber users try this before. Do
you have any luck? My protein has 250 residues. Any suggestion is greatly
appreciated.

Yours truly,

Jian Hui Wu