Re: Patch information for 1TUB.pdb in order to use "psfgen"

From: Roy Fernando (
Date: Tue Dec 10 2013 - 10:07:22 CST

Hi Lili,

The nature of the patch you want to add will be depending on the structure
of your protein. If the protein is simply the peptide chain you do not need
to add patches. In that case you can simply use a psfgen file similar to
what is in the NAMD tutorial to generate your psf file.

Depending on the nature of the additional structures you will either have
to make your own patches or use some standard patches (like sulfide brides)
available in the topology file.

You will find information in NAMD tutorial appendix (Topology file section)
and in Topology file tutorial (separate).


On Tue, Dec 10, 2013 at 10:21 AM, Lili Zhang <> wrote:

> Dear Everyone,
> I am here asking for some advice: I have downloaded one pdb file 1TUB.pdb,
> but I am not clear where to find the patching rules (if there is any) to
> apply in order to get the psf file.
> I am not sure what is the proper patch, and what residues I should apply
> the patch.
> Thank you very much for your help,
> Lili

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