AMBER Archive (2003)

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

From: Junmei Wang (JWang_at_encysive.com)
Date: Thu Aug 21 2003 - 15:16:02 CDT

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:

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 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 SG s S 12 11 8 2.383 114.949 35.990 0.00000
  14 CB c3 3 13 12 11 1.912 102.951 -154.363 0.00000
  15 CA c3 3 14 13 12 1.527 113.148 -85.892 0.00000
  16 HA1 hc E 15 14 13 1.100 104.829 53.205 0.00000
  17 HA2 hc E 15 14 13 1.100 111.122 179.997 0.00000
  18 HA3 hc E 15 14 13 1.101 104.818 -53.225 0.00000
  19 HB3 h1 E 14 13 12 1.090 107.599 35.187 0.00000
  20 HB2 h1 E 14 13 12 1.090 107.575 153.038 0.00000
  21 SG s S 12 11 8 2.421 117.068 -105.203 0.00000
  22 CB c3 3 21 12 11 1.913 102.633 16.976 0.00000
  23 CA c3 3 22 21 12 1.526 111.967 -136.746 0.00000
  24 HA1 hc E 23 22 21 1.100 104.812 53.252 0.00000
  25 HA2 hc E 23 22 21 1.100 111.081 -179.993 0.00000
  26 HA3 hc E 23 22 21 1.100 104.812 -53.232 0.00000
  27 HB3 h1 E 22 21 12 1.090 108.172 -15.994 0.00000
  28 HB2 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 CB c3 3 30 29 12 1.509 122.000 -1.576 0.00000
  32 CA c3 3 31 30 29 1.526 115.012 -179.982 0.00000
  33 HA1 hc E 32 31 30 1.100 104.832 53.195 0.00000
  34 HA2 hc E 32 31 30 1.100 111.103 -179.964 0.00000
  35 HA3 hc E 32 31 30 1.100 104.757 -53.232 0.00000
  36 HB2 hc E 31 30 29 1.090 106.657 58.386 0.00000
  37 HB3 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
    C CG ND1 CE1
  CD2 CB CG ND1
   CG HD2 CD2 NE2
  CD2 CE1 NE2 HE2
  HE1 ND1 CE1 NE2

DONE
STOP

                                                                           
             Natasja
             Brooijmans
             <nbrooij_at_itsa.ucs To
             f.edu> Qiang Lu <qiangl_at_uci.edu>
             Sent by: cc
             owner-amber_at_scrip "David A. Case" <amber_at_scripps.edu>
             ps.edu Subject
                                       Re[2]: AMBER: antechamber problem
                                                                           
             08/20/2003 05:26
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

I think the problem is that not all the atom names are unique.

Natasja Brooijmans, Ph.D.
Visiting Post-Doctoral Scholar
Kuntz Laboratory
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-2240
phone: 415-476 3986
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

On Wed, 20 Aug 2003, Qiang Lu wrote:

> Hi David,
>
> Bellow is the pdb file. Although there is a ZN, it doesn't matter, you
> can delete it.
>
> ATOM 1 CA ZNF 1 0.046 4.191 -0.713 1.00 0.00
> ATOM 2 1HA ZNF 1 -0.561 3.587 -0.022 1.00 0.00
> ATOM 3 2HA ZNF 1 0.434 5.144 -0.324 1.00 0.00
> ATOM 4 CB ZNF 1 1.185 3.268 -1.141 1.00 0.00
> ATOM 5 3HB ZNF 1 1.826 3.060 -0.284 1.00 0.00
> ATOM 6 2HB ZNF 1 1.770 3.751 -1.923 1.00 0.00
> ATOM 7 SG ZNF 1 0.570 1.590 -1.828 1.00 0.00
> ATOM 8 3HA ZNF 1 -0.614 4.249 -1.591 1.00 0.00
> ATOM 9 CA ZNF 1 -4.603 0.555 -0.722 1.00 0.00
> ATOM 10 HA1 ZNF 1 -5.046 -0.243 -0.108 1.00 0.00
> ATOM 11 HA2 ZNF 1 -4.974 1.576 -0.547 1.00 0.00
> ATOM 12 CB ZNF 1 -3.103 0.463 -0.459 1.00 0.00
> ATOM 13 2HB ZNF 1 -2.574 1.146 -1.124 1.00 0.00
> ATOM 14 3HB ZNF 1 -2.898 0.735 0.577 1.00 0.00
> ATOM 15 CG ZNF 1 -2.500 -0.904 -0.674 1.00 0.00
> ATOM 16 ND1 ZNF 1 -1.133 -1.154 -0.474 1.00 0.00
> ATOM 17 ZN ZNF 1 0.466 0.194 0.108 1.00 0.00
> ATOM 18 CE1 ZNF 1 -0.914 -2.437 -0.742 1.00 0.00
> ATOM 19 HE1 ZNF 1 0.091 -2.849 -0.650 1.00 0.00
> ATOM 20 NE2 ZNF 1 -2.044 -2.998 -1.093 1.00 0.00
> ATOM 21 HE2 ZNF 1 -2.150 -3.970 -1.347 1.00 0.00
> ATOM 22 CD2 ZNF 1 -3.058 -2.081 -1.064 1.00 0.00
> ATOM 23 HD2 ZNF 1 -4.071 -2.381 -1.330 1.00 0.00
> ATOM 24 HA3 ZNF 1 -4.735 0.150 -1.736 1.00 0.00
> ATOM 25 CA ZNF 1 -0.295 -0.967 3.883 1.00 0.00
> ATOM 26 1HA ZNF 1 -0.513 -1.489 2.940 1.00 0.00
> ATOM 27 2HA ZNF 1 0.190 -1.559 4.673 1.00 0.00
> ATOM 28 CB ZNF 1 0.570 0.225 3.479 1.00 0.00
> ATOM 29 3HB ZNF 1 1.530 -0.132 3.107 1.00 0.00
> ATOM 30 2HB ZNF 1 0.732 0.867 4.345 1.00 0.00
> ATOM 31 SG ZNF 1 -0.220 1.296 2.106 1.00 0.00
> ATOM 32 3HA ZNF 1 -1.277 -0.533 4.125 1.00 0.00
> ATOM 33 CA ZNF 1 4.153 -1.996 -1.665 1.00 0.00
> ATOM 34 1HA ZNF 1 3.288 -2.502 -2.119 1.00 0.00
> ATOM 35 2HA ZNF 1 4.925 -1.626 -2.355 1.00 0.00
> ATOM 36 CB ZNF 1 3.553 -0.854 -0.849 1.00 0.00
> ATOM 37 3HB ZNF 1 3.099 -0.126 -1.521 1.00 0.00
> ATOM 38 2HB ZNF 1 4.338 -0.371 -0.267 1.00 0.00
> ATOM 39 SG ZNF 1 2.206 -1.470 0.361 1.00 0.00
> ATOM 40 3HA ZNF 1 4.474 -2.737 -0.918 1.00 0.00
> TER
> END
> --
> Best regards,
> Qiang mailto:qiangl_at_uci.edu
>
>
> =================Original message text===============
> On Wed, Aug 20, 2003, Qiang Lu wrote:
> >
> > When I convert from pdb to prepin file, it only convert 18 atoms, other
> > 22 are labeled X like follow
> > I think I need to increase the limit of antechamber, could you please
> > tell me how to do it.
>
> We can't help you without more information; you probably need to send the
pdb
> file you used (or look to see if there is something odd after atom # 18).
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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