Subject: CHARMM QM/MM question

From: HU lihong <lhhu)at(yangtze.hku.hk>
Date: Tue, 15 Jun 2004 12:12:41 +0800 (HKT)

Dear All,

I am trying to calculate a biomolecule using QM/MM in c29b2, I need at 
least 3 link atoms. I don't know if it is ok with multiple link atoms 
since all of the examples only have one link atom. My calculation could be 
run but if I use the keyword energy which try to print the energy with QM 
calculation, it would be failed by segametational fault. Is that because 
my QM atoms are too much or the script what I wrote is not ok?

This is the QM/MM calcultion script in my calculation

-------------------------------------------------------------------------------------
nbonds -
atom shift vswitch eps 1.0 -
cutnb 999.0 ctofnb 998.0 ctonnb 997.0 e14fac 1.0

addl qqh1 pwdm A48 c pwdm A48 c
addl qqh2 pwdf A111 c pwdf A111 c
addl qqh3 pwdl A300 c pwdl A300 c

defind qmset sele segi pwdm .or. segi pwdf .or. segi pwdl end 

quan sele qmset end am1
---------------------------------------------------------------------------------------
And I want to know if it is all right that I just give the parameters for 
qqh atom like the example files. If it is not right, where I can find the 
correct parameters. Or can I find a more complex example of QM/MM than 
examples?

I'll appreciate your any kind help,

Yours sincerely,

Holly