AMBER Archive (2003)

Subject: Re: AMBER: Zn in antechamber

From: Junmei Wang (JWang_at_encysive.com)
Date: Mon Sep 29 2003 - 11:38:09 CDT

If you will make force constants 0.0, it doesn't matter what types they
are. You may just use "1". You may manually revise resp input files by
yourself. The amber7 version of respgen doesn't read in total charge
information from ac input files (If I remember correctly). 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
                                       Re: AMBER: Zn in antechamber
             09/29/2003 10:59
             AM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

Thanks. So what number (bond type) should I use for Zn-S, Zn-O, Zn-N?
And when I use respen, how can I constrain total charge as +2, instead
of 0?

Best,
Lishan

On Mon, 2003-09-29 at 11:32, Junmei Wang wrote:
>
>
>
> In ac file, the bond record is like this:
>
> BOND 1 1 2 1 C1 C2
>
> Field 1: bond flag
> Field 2: id, the sequence order is not important
> Field3: atom id of the first atom, important
> Field4: atom id of the second atom, important
> Field 5: bond type, defined in am1-bcc
> Field6: atom name of the first atom, can be omitted
> Field7: atom name of the second atom, can be omitted
>
> 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
> Re: AMBER: Zn in antechamber
> 09/29/2003 10:13
> AM
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
>
>
>
> Hi:
> How did you add four bonds there? I look at the ac file(the bond
> part):
> BOND 1 1 2 1 C1 C2
> What does the fourth number mean?
>
> Lishan
>
>
> On Fri, 2003-09-26 at 13:00, Junmei Wang wrote:
> >
> >
> >
> > 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_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
> > Re: AMBER: Zn in antechamber
> > 09/26/2003 10:01
> > AM
> >
> >
> > Please respond to
> > amber_at_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_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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> > >
> > >
> > >
> > >
> > >
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> > --
> > Lishan Yao <yaolisha_at_pilot.msu.edu>
> > MSU
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
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> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> --
> Lishan Yao <yaolisha_at_pilot.msu.edu>
> MSU
>
>
> -----------------------------------------------------------------------
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> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
>
>
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--
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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