AMBER Archive (2005)

Subject: AMBER:

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Tue Apr 19 2005 - 21:57:44 CDT

Dear all

I have some question about PARSE radii for Zn2+ and Ca2+

file "atmtypenumbers" gives atomic radius taken form Connolly "ms.explicit.rad" file
radius 18 1.74 1.97 # Ca calcium
radius 19 1.25 1.40 # Zn zinc (traditional radius)

file "parm99.dat" gives us VDW radius
  C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)
  Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,8262,(1991)

When running MM-PBSA, two line for Zn2+ and Ca2+ parse radii should be added into "my_parse_delphi.siz"
which number should I take for Zn and Ca?
if any of them shouldn't be taken, where can I find the Zn and Ca parse radii?

!my siz based on PARSE
!(value for P taken from Pauling,
! for Mg from Biophys J 2001, 80, 1151)
atom__res_radius_
O 1.4
H 1.0
1H 1.0
2H 1.0
3H 1.0
C 1.7
N 1.5
S 1.85
P 1.90
Mg 0.99
Zn 1.10 ????
C0 1.71 ????

any comment would be appreciated.

Best regard!

Yong Xu
yxu_at_mail.sioc.ac.cn
2005-04-20

===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* xuyongch_at_yahoo.com
===========================================================

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