Please try the latest code if you can. I have revised some codes to handle
metals recently. If you would like to send me your ac or mol2 file, I can
test it. If you use antechamber in amber7, you still can generate a prep
file for metal-organic molecule with a complete ac file, I mean, you need
manually add some bond information and revise some atom types, then you run
prepgen, instead of antechamber to get the prep input file.
Best
Junmei
===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang.tbc.com
Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================
Lishan Yao
<yaolisha.pilot.m
su.edu> To
Sent by: amber.scripps.edu
owner-amber.scrip cc
ps.edu
Subject
AMBER: Zn in antechamber
09/26/2003 08:48
AM
Please respond to
amber.scripps.edu
Hi there:
I try to get charges for a Znic-organic molecule complex by using
antechamber from a gaussian output. But it seems antechamber can not
identify Znic. It always puts 'DU' as the atom name for Zn. I changed
the code a little by adding Zn to the place wherever Fe shows up. Then I
don't get any complain, but I get this output:
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 C1 c3 M 3 2 1 1.540 111.208 180.000 -0.420
5 H1 hc E 4 3 2 1.097 113.409 138.220 0.142
6 H2 hc E 4 3 2 1.097 121.685 -88.895 0.142
7 H3 hc E 4 3 2 1.094 22.961 -143.963 0.142
8 C2 ca M 4 3 2 1.495 87.585 25.622 0.277
9 N1 nb M 8 4 3 1.402 123.456 -177.157 -0.407
10 C4 ca M 9 8 4 1.342 107.133 -179.520 0.110
11 H5 h5 E 10 9 8 1.081 126.444 -179.630 0.164
12 N2 na M 10 9 8 1.339 109.622 -0.091 -0.198
13 H4 hn E 12 10 9 1.015 125.306 -179.881 0.391
14 C3 ca M 12 10 9 1.381 108.894 -0.021 -0.260
15 H14 h4 E 14 12 10 1.080 122.140 -179.984 0.266
16 X 1 0 1 6.161 nan 706.048 0.000
17 X 1 0 1 6.161 nan 706.048 0.000
18 X 1 0 1 6.161 nan 706.048 0.000
19 X 1 0 1 6.161 nan 706.048 0.000
20 X 1 0 1 6.161 nan 706.048 0.000
21 X 1 0 1 6.161 nan 706.048 0.000
22 X 1 0 1 6.161 nan 706.048 0.000
23 X 1 0 1 6.161 nan 706.048 0.000
24 X 1 0 1 6.161 nan 706.048 0.000
25 X 1 0 1 6.161 nan 706.048 0.000
26 X 1 0 1 6.161 nan 706.048 0.000
27 X 1 0 1 6.161 nan 706.048 0.000
28 X 1 0 1 6.161 nan 706.048 0.000
29 X 1 0 1 6.161 nan 706.048 0.000
30 X 1 0 1 6.161 nan 706.048 0.000
31 X 1 0 1 6.161 nan 706.048 0.000
It looks like antechamber still couldn't identify Zn. So what should I
do?
Lishan
--
Lishan Yao <yaolisha.pilot.msu.edu>
MSU
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Received on Fri Sep 26 2003 - 16:53:01 PDT
