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.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.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.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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Received on Wed Aug 20 2003 - 23:53:01 PDT
