From: Fred (Rui FENG) (
Date: Wed Jul 02 2008 - 20:55:07 CDT

Hi Axel,

I followed your direction and it's ok now. I rewrote the PDB file and
exactly obey the PDB format (right value in the right column).

I just want to use NAMD to compute a pretty large system. The system
consists of many water spheres which are much larger than water
molecules. I think the PDB format is a bit old because the coordinate
format is just real(8,3). I may save the outputs in binary format to
keep the precision.

Thank you and have a nice day!


On Wed, Jul 2, 2008 at 5:36 PM, Axel Kohlmeyer
<> wrote:
> On Wed, 2 Jul 2008, Fred (Rui FENG) wrote:
> RF> Hi All,
> hi fred,
> RF> I'm using VMD 1.8.6. I'd like to draw a circle. The circle consists of
> RF> 154 atoms. Its center is ( 0, 0, 0 ), and the radius is 6,500
> RF> Angstrom. The circle is in the YZ plane. The PDB file is in the
> RF> attachment.
> RF>
> RF> I use the command "mol new test.pdb type pdb start 0 end 0 step 1
> RF> autobonds off" to open the PDB file. The problem is the output is not
> RF> a circle, but a line!
> that is because your pdb file is not conforming
> to the pdb standard and VMD honors it.
> try writing the same object in, e.g. .xyz format and it works.
> if you just want to draw some spheres or lines somewhere,
> why not use graphics/draw commands?
> cheers,
> axel.
> RF>
> RF> Do you think the size of the radius has exceeded the limitation of
> RF> VMD? What's the biggest size in VMD? Or is there anything wrong in the
> RF> PDB file?
> RF>
> RF> Thank you so much!
> RF>
> RF> Fred
> RF>
> --
> =======================================================================
> Axel Kohlmeyer
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.