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.mail.sioc.ac.cn
2005-04-20
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* 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.mail.sioc.ac.cn
* xuyongch.yahoo.com
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Received on Wed Apr 20 2005 - 04:53:00 PDT
