Dear amber-users
I want to simulate one protein with Zn2+ and Ca2+ ions. Althogh there are Zn and Ca parameter in Amber7.0 but when Xleap read protein_Zn_Ca.pdb, Xleap still cann't recoginise those kinds of atoms. So I must prepare Zn and Ca parameter seperately with protein.
following is the procedure I have done. please correct me if this step-by-step process is wrong.
if there are other way to produce a more common Zn.lib and Ca.lib, please don't hesitate to show me.
==my Zn_Ca.pdb
ATOM 1239 Zn Zn 1 1.069 -8.424 1.759 1.00 10.99
ATOM 1240 Zn Zn 2 -7.068 -7.322 -7.248 1.00 17.45
ATOM 1241 C0 Ca 3 -11.753 -9.470 2.693 1.00 16.46
ATOM 1242 C0 Ca 4 0.260 -0.183 -12.951 1.00 12.98
ATOM 1243 C0 Ca 5 -16.568 -0.908 2.699 1.00 8.46
==Zn.pdb
ATOM 1239 Zn Zn 1 1.069 -8.424 1.759 1.00 10.99
ATOM 1240 Zn Zn 2 -7.068 -7.322 -7.248 1.00 17.45
==Ca.pdb
ATOM 1241 C0 Ca 3 -11.753 -9.470 2.693 1.00 16.46
ATOM 1242 C0 Ca 4 0.260 -0.183 -12.951 1.00 12.98
ATOM 1243 C0 Ca 5 -16.568 -0.908 2.699 1.00 8.46
%Xleap&
xleap> source leaprc.ff99
xleap> source leaprc.gaff
xleap> Zn = loadpdb Zn.pdb
xleap> Ca = loadpdb Ca.pdb
xleap> edit Zn
editor> select Zn
editor> edit --> edit selected atoms
Name type Charge element
Zn Zn 2.000 Zn
Zn Zn 2.000 Zn
save and exit
xleap> saveoff Zn Zn.lib
xleap> loadoff Zn.lib
xleap> saveamberparams Zn Zn.top Zn.crd --->(so we got Zn parm)
=for Ca2+
edit Ca
Name type charge element
C0 C0 2.000 Ca
C0 C0 2.000 Ca
C0 C0 2.000 Ca
xleap> saveoff Ca Ca.lib
xleap> loadoff Ca.lib
xleap> saveamberparams Ca Ca.top Ca.crd
---> so we got Ca parm
if I want to recognise Zn or Ca in other protein, I must follow above step to prepare my top file.
So I want to know a best way to prepare a more common Zn.lib.
I am now using Amber 7.
Best regard!
Yong Xu
yxu.mail.sioc.ac.cn
2004-12-10
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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
* yxuemail.sina.com
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Received on Fri Dec 10 2004 - 07:53:01 PST
