VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Dec 08 2006 - 15:19:26 CST

As an aside, if your primary interest is being able to color things by a
floating point number, you can fill in the beta or occupancy fields of a
pdb file with floating point values; these are read by VMD.
Peter

Marcos Sotomayor wrote:
>
> Hi Paul,
>
> Have a look at the appendices of the NAMD tutorial available at:
>
> http://www.ks.uiuc.edu/Training/Tutorials/
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
>
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node21.html
>
>
> Marcos
>
> On Fri, 8 Dec 2006, Paul T. Bauman wrote:
>
>> Hello,
>>
>> I'm trying to generate .psf file from my own molecular simulation
>> code and I can't find the specific detais of the file format so VMD
>> will accept it. Does anyone know where I can look to get the most
>> detailed account of what VMD wants in the .psf file?
>>
>> Basically, I'm visualizing position of atoms as well as covalent
>> bonds using a .pdb format. Now, I want to color the atoms according
>> to a real valued number that I give it and I gather the best way to
>> hack it is to use a .psf file and specify my number as the charge and
>> plot the color according to charge. I've found a few examples here
>> and there of a .psf but I haven't gotten the format right yet (i.e.
>> VMD errors when it trys to read my version of the .psf file). Any
>> help is most appreciated. Thanks,
>>
>> Paul
>>