As I know, you can not have separated fragments in a prep file. To make it
work, you may add some bonds to link the fragments. For your molecules, I
added four bonds (Zn-N1, Zn-O1, Zn-S1, Zn-S2). If you do not want to those
bonds there at all, you may make all the force constants involved Zn 0.0.
Another solution is to make each fragment a residue ...
The following is the prep input file I generated with prepgen using the
modified ac file (adding four bonds). Be careful, I didn't revise atom
types and charges.
Best
Junmei
0 0 2
This is a remark line
molecule.res
MOL INT 0
CORRECT OMIT DU BEG
0.0000
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 C5 C M 3 2 1 1.540 111.208 180.000 0.00000
5 H6 H E 4 3 2 1.090 114.786 -171.575 0.00000
6 H7 H E 4 3 2 1.092 128.058 39.003 0.00000
7 H8 H E 4 3 2 1.091 75.841 -64.597 0.00000
8 S1 S M 4 3 2 1.849 32.300 96.859 0.00000
9 H15 H E 8 4 3 1.351 99.206 160.047 0.00000
10 Zn1 Zn M 8 4 3 2.439 110.077 54.129 0.00000
11 O1 O B 10 8 4 2.121 103.435 -41.564 0.00000
12 H12 H E 11 10 8 0.974 129.534 81.245 0.00000
13 H13 H E 11 10 8 0.975 123.379 -100.277 0.00000
14 S2 S B 10 8 4 2.417 112.108 64.107 0.00000
15 C6 C 3 14 10 8 1.851 109.565 78.717 0.00000
16 H9 H E 15 14 10 1.089 111.686 45.804 0.00000
17 H10 H E 15 14 10 1.092 106.733 -75.548 0.00000
18 H11 H E 15 14 10 1.091 107.147 167.695 0.00000
19 H16 H E 14 10 8 1.351 99.413 -178.154 0.00000
20 N1 N M 10 8 4 1.983 109.675 -151.106 0.00000
21 C2 C M 20 10 8 1.402 128.203 -177.177 0.00000
22 C1 C 3 21 20 10 1.495 123.456 1.125 0.00000
23 H1 H E 22 21 20 1.097 111.658 68.569 0.00000
24 H2 H E 22 21 20 1.097 112.019 -53.788 0.00000
25 H3 H E 22 21 20 1.094 110.154 -172.849 0.00000
26 C3 C M 21 20 10 1.369 107.648 -179.186 0.00000
27 H14 H E 26 21 20 1.080 131.157 179.945 0.00000
28 N2 N M 26 21 20 1.381 106.702 -0.179 0.00000
29 H4 H E 28 26 21 1.015 125.800 179.985 0.00000
30 C4 C M 28 26 21 1.339 108.894 0.126 0.00000
31 H5 H E 30 28 26 1.081 123.932 179.533 0.00000
LOOP
C4 N1
IMPROPER
C2 C4 N1 Zn1
C1 C3 C2 N1
C2 H14 C3 N2
C3 C4 N2 H4
H5 N1 C4 N2
DONE
STOP
===============================================================
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
Re: AMBER: Zn in antechamber
09/26/2003 10:01
AM
Please respond to
amber.scripps.edu
Hi:
The antechamber I use is from amber7. But I don't know whether it is
a latest code or not. Here is the ac file I get. It may not be right,
because when I run antechamber, I saw "segmentation fault" on the
screen. And the charge I give is +2, but the output gives me 0.
Lishan
CHARGE 0.00
Formula: H16C6N2O1S2Zn1
ATOM 1 C1 MOL 1 -2.562 1.661 0.819 0.000000
C C
ATOM 2 C2 MOL 1 -2.625 0.314 0.173 0.000000
C C
ATOM 3 N1 MOL 1 -1.490 -0.452 -0.130 0.000000
N N
ATOM 4 C3 MOL 1 -3.724 -0.394 -0.233 0.000000
C C
ATOM 5 C4 MOL 1 -1.920 -1.585 -0.706 0.000000
C C
ATOM 6 N2 MOL 1 -3.257 -1.573 -0.779 0.000000
N N
ATOM 7 C5 MOL 1 3.401 -1.894 0.294 0.000000
C C
ATOM 8 S1 MOL 1 1.838 -1.776 -0.687 0.000000
S S
ATOM 9 C6 MOL 1 1.225 2.784 -1.725 0.000000
C C
ATOM 10 S2 MOL 1 1.425 2.170 0.010 0.000000
S S
ATOM 11 Zn1 MOL 1 0.413 -0.015 0.217 0.000000
Zn Zn
ATOM 12 O1 MOL 1 0.592 -0.265 2.316 0.000000
O O
ATOM 13 H1 MOL 1 -2.126 2.412 0.148 0.000000
H H
ATOM 14 H2 MOL 1 -1.986 1.643 1.752 0.000000
H H
ATOM 15 H3 MOL 1 -3.569 2.006 1.070 0.000000
H H
ATOM 16 H4 MOL 1 -3.830 -2.314 -1.171 0.000000
H H
ATOM 17 H5 MOL 1 -1.304 -2.400 -1.058 0.000000
H H
ATOM 18 H6 MOL 1 3.858 -0.915 0.439 0.000000
H H
ATOM 19 H7 MOL 1 4.074 -2.562 -0.247 0.000000
H H
ATOM 20 H8 MOL 1 3.134 -2.348 1.250 0.000000
H H
ATOM 21 H9 MOL 1 0.210 2.633 -2.091 0.000000
H H
ATOM 22 H10 MOL 1 1.945 2.237 -2.337 0.000000
H H
ATOM 23 H11 MOL 1 1.489 3.843 -1.724 0.000000
H H
ATOM 24 H12 MOL 1 1.294 0.039 2.919 0.000000
H H
ATOM 25 H13 MOL 1 -0.077 -0.718 2.861 0.000000
H H
ATOM 26 H14 MOL 1 -4.778 -0.162 -0.182 0.000000
H H
ATOM 27 H15 MOL 1 2.325 -1.184 -1.799 0.000000
H H
ATOM 28 H16 MOL 1 0.469 2.914 0.609 0.000000
H H
BOND 1 1 2 1 C1 C2
BOND 2 1 13 1 C1 H1
BOND 3 1 14 1 C1 H2
BOND 4 1 15 1 C1 H3
BOND 5 2 3 7 C2 N1
BOND 6 2 4 8 C2 C3
BOND 7 3 5 8 N1 C4
BOND 8 4 6 7 C3 N2
BOND 9 4 26 1 C3 H14
BOND 10 5 6 7 C4 N2
BOND 11 5 17 1 C4 H5
BOND 12 6 16 1 N2 H4
BOND 13 7 8 1 C5 S1
BOND 14 7 18 1 C5 H6
BOND 15 7 19 1 C5 H7
BOND 16 7 20 1 C5 H8
BOND 17 8 27 1 S1 H15
BOND 18 9 10 1 C6 S2
BOND 19 9 21 1 C6 H9
BOND 20 9 22 1 C6 H10
BOND 21 9 23 1 C6 H11
BOND 22 10 28 1 S2 H16
BOND 23 12 24 1 O1 H12
BOND 24 12 25 1 O1 H13
On Fri, 2003-09-26 at 10:47, Junmei Wang wrote:
>
>
>
> 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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>
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>
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--
Lishan Yao <yaolisha.pilot.msu.edu>
MSU
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Received on Fri Sep 26 2003 - 18:53:01 PDT
