AMBER Archive (2006)

Subject: AMBER: ZN prepin

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 26 2006 - 16:29:31 CST

Dear all, I used the following methods of Junmei, and
I got the UI.ac file from a CYM_ZN.pdb. In the
original message, Junmei uses command: antechamber -fi
pdb -fo ac -i znf.pdb -o znf.ac. But for my pdb file,
bu that command cannot give the right UIO.ac file
because the bondtype command cannot be executed, thus
in the command I add -j 0.

>From the attached UI.ac file, I got the attached
prepin file, then I got the frcmod. But for the frcmod
file, it needs some "ATTN, need revision".

Will you please tell me how can I make these
"revisions"?

In addition, from the prepin file, we cannot get any
charge information. Will you please tell me in the
"antechamber -fi pdb -fo ac -i znf.pdb -o znf.ac"
command, what kind of charge methods should we use?

I am looking forward to getting your reply.

Best regards.

Fenghui Fan

--- Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:

> Hi, Dave,
>
>
> I am sorry, actually the prep file in my previous
> email is an old one
> (generated without atom name duplication check, I
> got
> this file long time
> ago). In default, the new version of antechamber
> does
> check atomtype
> duplication and do corrections. The following is
> what
> I did:
> (1) run antechamber to get an ac file
> antechamber -fi pdb -fo ac -i znf.pdb -o
> znf.ac
> (2) In znf.ac, manually change atom type of Zn from
> DU
> to zn (gaff does
> not have zn atom type)
> (3) In znf.ac, manually add bond information
> involved
> by Zn (antechamber
> does not have radius parameter for zn in
> $AMBERHOME/dat/antechamber/CONNECT.TPL, so cannot
> judge if bonds formed or
> not).
>
>
> BOND 37 16 17
> BOND 38 17 7
> BOND 39 17 31
> BOND 40 17 39
>
>
> (4) run antechamber or prepgen to get prep file
> antechamber -fi ac -fo prepi -i znf.ac -o
> znf.prep -j 0
> or
> prepgen -i znf.ac -o znf.prei -f int
>
>
> The following is znf.ac and znf.prep.
>
>
> Best
>
>
> Junmei
>
>
> znf.ac
>
>
> CHARGE 0.00 ( 0 )
> Formula: H23 C11 N2 S3 Zn1
> ATOM 1 CA ZNF 1 0.046 4.191 -0.713 0.000000 c3
> ATOM 2 HA1 ZNF 1 -0.561 3.587 -0.022 0.000000 hc
> ATOM 3 HA2 ZNF 1 0.434 5.144 -0.324 0.000000 hc
> ATOM 4 CB ZNF 1 1.185 3.268 -1.141 0.000000 c3
> ATOM 5 HB3 ZNF 1 1.826 3.060 -0.284 0.000000 h1
> ATOM 6 HB2 ZNF 1 1.770 3.751 -1.923 0.000000 h1
> ATOM 7 SG ZNF 1 0.570 1.590 -1.828 0.000000 s
> ATOM 8 HA3 ZNF 1 -0.614 4.249 -1.591 0.000000 hc
> ATOM 9 C1 ZNF 1 -4.603 0.555 -0.722 0.000000 c3
> ATOM 10 H1 ZNF 1 -5.046 -0.243 -0.108 0.000000 hc
> ATOM 11 H4 ZNF 1 -4.974 1.576 -0.547 0.000000 hc
> ATOM 12 C4 ZNF 1 -3.103 0.463 -0.459 0.000000 c3
> ATOM 13 H10 ZNF 1 -2.574 1.146 -1.124 0.000000 hc
> ATOM 14 H7 ZNF 1 -2.898 0.735 0.577 0.000000 hc
> ATOM 15 CG ZNF 1 -2.500 -0.904 -0.674 0.000000 c2
> ATOM 16 ND1 ZNF 1 -1.133 -1.154 -0.474 0.000000 n2
> ATOM 17 Zn ZNF 1 0.466 0.194 0.108 0.000000 zn
> (change atom type)
> ATOM 18 CE1 ZNF 1 -0.914 -2.437 -0.742 0.000000 c2
> ATOM 19 HE1 ZNF 1 0.091 -2.849 -0.650 0.000000 h5
> ATOM 20 NE2 ZNF 1 -2.044 -2.998 -1.093 0.000000 na
> ATOM 21 HE2 ZNF 1 -2.150 -3.970 -1.347 0.000000 hn
> ATOM 22 CD2 ZNF 1 -3.058 -2.081 -1.064 0.000000 c2
> ATOM 23 HD2 ZNF 1 -4.071 -2.381 -1.330 0.000000 h4
> ATOM 24 H13 ZNF 1 -4.735 0.150 -1.736 0.000000 hc
> ATOM 25 C2 ZNF 1 -0.295 -0.967 3.883 0.000000 c3
> ATOM 26 H2 ZNF 1 -0.513 -1.489 2.940 0.000000 hc
> ATOM 27 H5 ZNF 1 0.190 -1.559 4.673 0.000000 hc
> ATOM 28 C5 ZNF 1 0.570 0.225 3.479 0.000000 c3
> ATOM 29 H8 ZNF 1 1.530 -0.132 3.107 0.000000 h1
> ATOM 30 H11 ZNF 1 0.732 0.867 4.345 0.000000 h1
> ATOM 31 S1 ZNF 1 -0.220 1.296 2.106 0.000000 s
> ATOM 32 H14 ZNF 1 -1.277 -0.533 4.125 0.000000 hc
> ATOM 33 C3 ZNF 1 4.153 -1.996 -1.665 0.000000 c3
> ATOM 34 H3 ZNF 1 3.288 -2.502 -2.119 0.000000 hc
> ATOM 35 H6 ZNF 1 4.925 -1.626 -2.355 0.000000 hc
> ATOM 36 C6 ZNF 1 3.553 -0.854 -0.849 0.000000 c3
> ATOM 37 H9 ZNF 1 3.099 -0.126 -1.521 0.000000 h1
> ATOM 38 H12 ZNF 1 4.338 -0.371 -0.267 0.000000 h1
> ATOM 39 S2 ZNF 1 2.206 -1.470 0.361 0.000000 s
> ATOM 40 H15 ZNF 1 4.474 -2.737 -0.918 0.000000 hc
> BOND 1 1 2 0 CA HA1
> BOND 2 1 3 0 CA HA2
> BOND 3 1 4 0 CA CB
> BOND 4 1 8 0 CA HA3
> BOND 5 4 5 0 CB HB3
> BOND 6 4 6 0 CB HB2
> BOND 7 4 7 0 CB SG
> BOND 8 9 10 0 C1 H1
> BOND 9 9 11 0 C1 H4
> BOND 10 9 12 0 C1 C4
> BOND 11 9 24 0 C1 H13
> BOND 12 12 13 0 C4 H10
> BOND 13 12 14 0 C4 H7
> BOND 14 12 15 0 C4 CG
> BOND 15 15 16 0 CG ND1
> BOND 16 15 22 0 CG CD2
> BOND 17 16 18 0 ND1 CE1
> BOND 18 18 19 0 CE1 HE1
> BOND 19 18 20 0 CE1 NE2
> BOND 20 20 21 0 NE2 HE2
> BOND 21 20 22 0 NE2 CD2
> BOND 22 22 23 0 CD2 HD2
> BOND 23 25 26 0 C2 H2
> BOND 24 25 27 0 C2 H5
> BOND 25 25 28 0 C2 C5
> BOND 26 25 32 0 C2 H14
> BOND 27 28 29 0 C5 H8
> BOND 28 28 30 0 C5 H11
> BOND 29 28 31 0 C5 S1
> BOND 30 33 34 0 C3 H3
> BOND 31 33 35 0 C3 H6
> BOND 32 33 36 0 C3 C6
> BOND 33 33 40 0 C3 H15
> BOND 34 36 37 0 C6 H9
> BOND 35 36 38 0 C6 H12
> BOND 36 36 39 0 C6 S2
> BOND 37 16 17 (add bond info)
> BOND 38 17 7 (add bond info)
> BOND 39 17 31 (add bond info)
> BOND 40 17 39 (add bond info)
>
>
>
> znf.prep
>
>
> 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 CA c3 M 3 2 1 1.540 111.208 180.000 0.00000
> 5 HA1 hc E 4 3 2 1.100 56.520 -48.843 0.00000
> 6 HA2 hc E 4 3 2 1.100 110.654 -157.795 0.00000
> 7 HA3 hc E 4 3 2 1.100 53.127 93.779 0.00000
> 8 CB c3 M 4 3 2 1.527 138.227 24.877 0.00000
> 9 HB3 h1 E 8 4 3 1.090 109.481 -122.693 0.00000
> 10 HB2 h1 E 8 4 3 1.090 109.492 117.306 0.00000
> 11 SG s M 8 4 3 1.915 112.996 -2.688 0.00000
> 12 Zn zn M 11 8 4 2.389 103.611 -90.106 0.00000
> 13 S1 s S 12 11 8 2.383 114.949 35.990 0.00000
> 14 C5 c3 3 13 12 11 1.912 102.951 -154.363 0.00000
>
> 15 C2 c3 3 14 13 12 1.527 113.148 -85.892 0.00000
> 16 H2 hc E 15 14 13 1.100 104.829 53.205 0.00000
> 17 H5 hc E 15 14 13 1.100 111.122 179.997 0.00000
> 18 H14 hc E 15 14 13 1.101 104.818 -53.225 0.00000
>
> 19 H8 h1 E 14 13 12 1.090 107.599 35.187 0.00000
> 20 H11 h1 E 14 13 12 1.090 107.575 153.038 0.00000
>
> 21 S2 s S 12 11 8 2.421 117.068 -105.203 0.00000
> 22 C6 c3 3 21 12 11 1.913 102.633 16.976 0.00000
> 23 C3 c3 3 22 21 12 1.526 111.967 -136.746 0.00000
>
> 24 H3 hc E 23 22 21 1.100 104.812 53.252 0.00000
> 25 H6 hc E 23 22 21 1.100 111.081 -179.993 0.00000
>
> 26 H15 hc E 23 22 21 1.100 104.812 -53.232 0.00000
>
> 27 H9 h1 E 22 21 12 1.090 108.172 -15.994 0.00000
> 28 H12 h1 E 22 21 12 1.090 108.187 102.496 0.00000
>
> 29 ND1 n2 M 12 11 8 2.171 100.233 150.834 0.00000
> 30 CG c2 M 29 12 11 1.404 130.150 -67.187 0.00000
> 31 C4 c3 3 30 29 12 1.509 122.000 -1.576 0.00000
> 32 C1 c3 3 31 30 29 1.526 115.012 -179.982 0.00000
>
> 33 H1 hc E 32 31 30 1.100 104.832 53.195 0.00000
> 34 H4 hc E 32 31 30 1.100 111.103 -179.964 0.00000
>
> 35 H13 hc E 32 31 30 1.100 104.757 -53.232 0.00000
>
> 36 H10 hc E 31 30 29 1.090 106.657 58.386 0.00000
> 37 H7 hc E 31 30 29 1.091 106.624 -58.421 0.00000
> 38 CD2 c2 M 30 29 12 1.360 106.636 178.434 0.00000
>
>
=== message truncated ===

 
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