VMD-L Mailing List

From: Dipesh Bhattarai (dipesh.bhattarai_at_gmail.com)
Date: Tue Mar 02 2010 - 21:41:53 CST

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