AMBER Archive (2003)

Subject: Re: AMBER: Zn in antechamber

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Sep 29 2003 - 10:59:09 CDT

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
> > >
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> > >
> > >
> > >
> > > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > 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
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > 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
>
>
> -----------------------------------------------------------------------
> 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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-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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