VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 19 2005 - 18:52:46 CDT

Hi,
  The currently available PDB plugin ignores CONECT records.
They fail for large structures which are commonly used in MD simulations,
so historically we use separate files such as PSF files to acquire this
information. I've been meaning to fix up CONECT record reading for
the PDB plugin but haven't done this just yet. You could construct a
PSF file pretty easily, and that would make VMD happy.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 19, 2005 at 07:04:31PM -0400, jiwu liu wrote:
>
> Dear list:
>
> I ran a MD simulation of bead-string model with LAMMPS, and want to
> visualize the structure with VMD. After reading previous mail from the list,
> I added "dump_modify ID header xyz" into LAMMPS input script to ask it dump
> a xyz file for visualization. Certainly, no bond is shown by VMD when I
> loaded the xyz file, which, as I knew from that instructive mail, is because
> xyz file doesn't have bonding information.
> So I think probably I can make a fake PDB file to tell the VMD about
> bonding information and use the xyz file as trajectory data. I constructed
> PDB file like below:
>
> CONECT 1 2
> CONECT 2 3
> ....
> ATOM 1 B BEA 1 0.000 0.000 0.000 1.00 1.00 BE20
> ATOM 2 B BEA 2 0.000 0.000 2.000 1.00 1.00 BE20
> ATOM 3 B BEA 3 0.000 0.000 4.000 1.00 1.00 BE20
> ATOM 4 B BEA 4 0.000 0.000 6.000 1.00 1.00 BE20
> .......
> END
>
> Again, VMD doesn't seem to understand this PDB file and draw a structure
> without bond. I wonder what's wrong with this PDB file. Why can't it be
> recagonized by VMD?
>
> Thanks!
>
> -jiwu 

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