VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Feb 24 2008 - 09:27:34 CST

This still depends on exactly what you're going to *do* with the new
residue (look at it, run MD, run continuum electrostatics calculations,
etc). If you want to do MD, for example, you should look at the topology
file tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/)
and follow a similar procedure. If you want to change a residue, you can
change its residue name to the new residue name and run the structure
through psfgen with the new topology file you've created.
VMD itself doesn't have a "residue library"; several of the tools have
their own ways of knowing what residues are available. psfgen, for
example, gets this information from a topology file.

Peter

fouchni_at_uni-osnabrueck.de wrote:
> Dear all,
>
> First of all I apology for resending my question to a mailing list and to
> individuals. I am new in the field and didn't know how things work. Coming
> back to my former question, I have a pdb file for a given structure
> (protein), and I would like to replace one or two residues in the
> structure with unkonwn residue. So how shall I add the unknown residue to
> residue library in VMD? My second question is how in general one can build
> a new residue (unsual residue)?
>
>
> Best regards,
> F. Ouchni
>
>