AMBER Archive (2005)

Subject: AMBER: example script for hbond calculation

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Jun 30 2005 - 01:27:15 CDT

Dear amber users below I have shown my script for
calculating hbons in micelle structure:-

trajin micelwat_md16_20.mdcrd

prnlev 2
#donor mask :1-27_at_O2',O3',O4',O5',O6'

donor mask :1-27_at_O2'
donor mask :1-27_at_O3'
donor mask :1-27_at_O4'
donor mask :1-27_at_O5'
donor mask :1-27_at_O6'

acceptor mask :1-27_at_O4 :1-27_at_H8
acceptor mask :1-27_at_O3 :1-27_at_H9
acceptor mask :1-27_at_O2 :1-27_at_H10
acceptor mask :1-27_at_O6 :1-27_at_H11

donor print
acceptor print

prnlev 0
hbond out output_hb2.dat \
        time 1.0 \
        angle 120.0 \
        distance 4.0
---------------------------------------------
My question:
1) what is the meaning of apostrophy (') every end of
atom name in donor line?

2) is there any different in writing the donor atoms
horizontal way or vertical way..?

3) in acceptor line do i need to put the symbol (')
end of Oxygen atom??

Wish anyone can help.
Thank you
Vijay

        
        
                
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