VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 29 2011 - 15:21:41 CDT

Hi,
  Once you exceed 99,999 atoms, the width of the PDB atom index
field is no longer big enough to store the index. The PDB plugins
switches to using hexadecimal numbering, since the file is no longer
truly PDB compliant at the point when it exceeds 99999 atoms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 29, 2011 at 03:07:27PM -0500, snoze pa wrote:
> Dear VMD users,
>
> Why I am getting following a,b.cd for Atom numbers using VMD
>
> ATOM 5992a H1 TIP3W7707 104.097 107.482 109.849 1.00 0.00
> WT35 H
> ATOM 5992b H2 TIP3W7707 102.662 107.721 110.076 1.00 0.00
> WT35 H
> ATOM 5992c OH2 TIP3W7876 106.850 104.513 155.693 1.00 0.00
> WT35 O
> ATOM 5992d H1 TIP3W7876 107.477 104.702 154.968 1.00 0.00
> WT35 H
> ATOM 5992e H2 TIP3W7876 106.603 103.602 155.555 1.00 0.00
> WT35 H
> ATOM 5992f OH2 TIP3W7961 102.749 104.963 117.549 1.00 0.00
> WT35 O
> ATOM 59930 H1 TIP3W7961 102.811 103.989 117.422 1.00 0.00
> WT35 H
> ATOM 59931 H2 TIP3W7961 103.734 105.135 117.788 1.00 0.00
> WT35 H
> ATOM 59932 OH2 TIP3W7978 105.354 106.795 167.038 1.00 0.00
> WT35 O
> ATOM 59933 H1 TIP3W7978 105.560 105.941 167.426 1.00 0.00
> WT35 H
> ATOM 59934 H2 TIP3W7978 104.729 106.650 166.319 1.00 0.00
> WT35 H
> ATOM 59935 OH2 TIP3W8009 104.982 104.832 140.735 1.00 0.00
> WT35 O
> ATOM 59936 H1 TIP3W8009 104.959 104.011 140.217 1.00 0.00
> WT35 H
> ATOM 59937 H2 TIP3W8009 105.894 105.031 140.696 1.00 0.00
> WT35 H
> ATOM 59938 OH2 TIP3W8270 104.155 105.004 164.551 1.00 0.00
> WT35 O
> ATOM 59939 H1 TIP3W8270 104.016 104.198 163.993 1.00 0.00
> WT35 H
> ATOM 5993a H2 TIP3W8270 103.967 105.805 164.002 1.00 0.00
> WT35 H
> ATOM 5993b OH2 TIP3W8290 107.129 106.421 146.396 1.00 0.00
> WT35 O
> ATOM 5993c H1 TIP3W8290 106.607 106.518 147.208 1.00 0.00
> WT35 H
> ATOM 5993d H2 TIP3W8290 108.017 106.646 146.685 1.00 0.00
> WT35 H
> ATOM 5993e OH2 TIP3W8411 106.015 104.409 117.639 1.00 0.00
> WT35 O
> ATOM 5993f H1 TIP3W8411 105.957 104.536 116.692 1.00 0.00
> WT35 H
> ATOM 59940 H2 TIP3W8411 106.987 104.482 117.870 1.00 0.00
> WT35 H
> ATOM 59941 OH2 TIP3W8412 110.778 106.429 140.744 1.00 0.00
> WT35 O
> ATOM 59942 H1 TIP3W8412 110.870 107.378 140.936 1.00 0.00
> WT35 H
> ATOM 59943 H2 TIP3W8412 110.514 106.460 139.777 1.00 0.00
> WT35 H
>
> Thank you
> S 

-- 
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