VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 09 2007 - 17:36:23 CDT

Hi,
  STRIDE wants the atom names to follow the PDB atom naming conventions.
If they do not, there's a good chance that it will terminate the calculation
since it can't understand the structure. I don't think that the temperature
factor plays any role, as far as I recall.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 09, 2007 at 03:49:58PM -0600, Jim Pfaendtner wrote:
> Hi,
>
> I have used CHARMM to build a complex of several proteins and the new
> proteins do not show secondary structure in VMD when I try to draw
> them with "ribbons or new cartoon". I noticed that the input pdb
> file has values for temperature factor (2.0 for H atoms and 5.0 for
> heavy atoms) whereas my new CHARMM output pdb file has all zeros for
> the temperature factor (column 63 in my pdb file).
>
> Could this be the reason Stride is not drawing the same secondary
> structure?
>
> Is there an easy way to generate the temperature factors using CHARMM
> or psfgen?
>
> Thank you,
> Jim 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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