AMBER Archive (2003)

Subject: Re: Re[2]: AMBER: antechamber problem

From: Junmei Wang (JWang_at_encysive.com)
Date: Fri Aug 22 2003 - 10:03:23 CDT

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
  39 HD2 h4 E 38 30 29 1.089 133.628 -179.944 0.00000
  40 NE2 na M 38 30 29 1.367 106.395 -0.041 0.00000
  41 HE2 hn E 40 38 30 1.010 124.942 179.950 0.00000
  42 CE1 c2 M 40 38 30 1.310 110.298 0.053 0.00000
  43 HE1 h5 E 42 40 38 1.090 131.017 179.972 0.00000

LOOP
  CE1 ND1

IMPROPER
   CG CE1 ND1 Zn
  CD2 C4 CG ND1
   CG HD2 CD2 NE2
  CD2 CE1 NE2 HE2
  HE1 ND1 CE1 NE2

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
===============================================================

                                                                           
             "David A. Case"
             <case_at_scripps.edu
> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       Re: Re[2]: AMBER: antechamber
             08/21/2003 06:34 problem
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

On Thu, Aug 21, 2003, Junmei Wang wrote:
>
> This molecule has a Zinc atom and amber7 cannot handle it properly.
Please
> try the latest version of antechamber in amber8, it should works given
the
> atom connectivity is good (one can always revise it from an ac or mol2
> file). Pay attention to atom names since the new version of antechamber
> automatically rename duplicated atom names. The following is the prepin
> file I generated:
>

Just a note: Junmei's prepin file (not shown here) still has duplicate
atom names in the same residue, and so will not work in LEaP. The only
solution I know of right now is to make the atom names unique by hand.

..dac 

--

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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