VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Apr 29 2008 - 11:44:04 CDT

Hi Fan,
autopsf is designed to make the average case easy, but what you're
talking about isn't the average case, so you may need to to this by hand
instead. It's probably good to do it by hand once anyway to make sure
you know how to go about building the cyclic peptide (which I've never
done). If all this involves is adding a single patch to two residues,
though, you should be able to just do it by adding the appropriate patch
to the appropriate residues in the autopsf gui.
Best,
Peter

Gao, Fan, Ph.D. wrote:
>
> Dear VMD users,
> I am new to VMD and just learned how to use Automatic PSF builder to
> create a psf file for a linear peptide.
> Right now, I am dealing with a small cyclic peptide (connection
> through the main chain).
> With the pdb file of this peptide in hand, what should I do to
> generate a psf file by using Automatic PSF builder?
>
> Thanks a lot.
>
> Fan
>