VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 03 2010 - 01:11:27 CST

Hi,
  Most simulation packages that work with PDB files as input accept
non-standard variants that exceed 99,999 atoms, either without atom
index numbers or with asterisks as shown in your example.
This will not cause any problem with NAMD, NAMD doesn't
pay attention to these indices anyway. There isn't
any truly legal way to emit a PDB structure with over 99,999 atoms
as a single model.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 03, 2010 at 02:52:07PM +0800, YangMingjun wrote:
> Dear Dipesh,
> Then how should I do when my system is larger than 100000 atoms?
>
> Many thanks.
> Mingjun
> 2010-03-03
> --------
> State Key Lab of Molecular Reaction Dynamics (SKLMRD),
> Dalian Institute of Chemical Physics (DICP),
> Chinese Academy of Sciences (CAS).
> Zhongshan Road457, Dalian City, 116023, China.
>
>
> ------------ At 2010-03-03 11:42:16 you wrote: -------------
> From: Dipesh Bhattarai
> Sent: 2010-03-03 11:42:16
> To: YangMingjun
> CC: vmd-l
> Subject: Re: vmd-l: display of the atom number beyond 100000 in pdb file
>
> I think this is due to the pdb file format. It only allows for 5 digit
> number. So basically you cannot have more than 99999 atoms.
>
> Dipesh
>
> On Tue, Mar 2, 2010 at 8:36 PM, YangMingjun <mjyang_at_dicp.ac.cn> wrote:
>
> > Dear all,
> > I created a system.pdb file corresponding to the system.psf file by VMD.
> > But the atom number beyond 100000 is not displayed normally.
> > Does it affect the subsequent MD simulation and energy minimization? Or how
> > to fix this problem for normally display?
> >
> > Part of the system.pdb file is:
> > -------
> > ...
> > ATOM 99996 OH2 TIP3 8931 13.511 28.315 -25.647 1.00 0.00 WT7
> > O
> > ATOM 99997 H1 TIP3 8931 13.491 29.246 -25.692 1.00 0.00 WT7
> > H
> > ATOM 99998 H2 TIP3 8931 13.733 28.131 -26.571 1.00 0.00 WT7
> > H
> > ATOM 99999 OH2 TIP3 8932 20.841 35.078 -29.982 1.00 0.00 WT7
> > O
> > ATOM ***** H1 TIP3 8932 20.462 35.696 -30.696 1.00 0.00 WT7
> > H
> > ATOM ***** H2 TIP3 8932 21.427 35.666 -29.452 1.00 0.00 WT7
> > H
> > ATOM ***** OH2 TIP3 8935 8.519 28.077 -34.237 1.00 0.00 WT7
> > O
> > ATOM ***** H1 TIP3 8935 9.441 28.048 -34.615 1.00 0.00 WT7
> > H
> > ATOM ***** H2 TIP3 8935 8.109 28.653 -34.850 1.00 0.00 WT7
> > H
> > ATOM ***** OH2 TIP3 8936 15.538 37.379 0.451 1.00 0.00 WT7
> > O
> > ATOM ***** H1 TIP3 8936 14.638 37.245 0.108 1.00 0.00 WT7
> > H
> > ...
> > -------
> >
> > Many thanks.
> >
> > Yang Mingjun
> >
> > 2010-03-03
> >
> > -----------------------------------------------
> >
> >
> >
> >
>
>
> --
> Dipesh Bhattarai, PhD
>
>
> ------------------------------------------------------
> 

-- 
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