VMD-L Mailing List

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Jun 29 2011 - 15:24:44 CDT

Hi John,
  Thank for your prompt reply. Just a quick question, so these Atom number
will not create any problem in NAMD simulation.

Thanks in advance
S

On Wed, Jun 29, 2011 at 3:21 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>