AMBER Archive (2003)

Subject: Re: AMBER: Zn in antechamber

From: Junmei Wang (JWang_at_encysive.com)
Date: Fri Sep 26 2003 - 09:47:45 CDT

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_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             Lishan Yao
             <yaolisha_at_pilot.m
             su.edu> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       AMBER: Zn in antechamber
             09/26/2003 08:48
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_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_at_pilot.msu.edu>
MSU

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