VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Jul 10 2008 - 11:17:46 CDT

You will need to create a patch in your topology file for this bond.
It actually shouldn't be too difficult as long as you carefully
follow the format of the other patches. The appendix of the NAMD
tutorial gives some additional details about their format. You might
also need to add bond, angle, and dihedral terms to your parameter
file before you can simulate it. NAMD will tell you though if
something is missing.

On Jul 10, 2008, at 8:56 AM, Jim Pfaendtner wrote:

> Dear vmd-l,
>
> I am trying to build a bicyclic polypeptide using psfgen and vmd.
> The first ring is created by joining the first and last residues
> with patch LINK, and this works without difficulty. The second
> ring is created because there is a nonstandard bond between two CYS
> and TRP residues as in phalloidin. The S atom in CYS bonds as if
> it was in a disulphide bridge, but it bonds with the CD1 atom of TRP.
>
> I have not found a straightforward way to do this with the patch
> command. Does anyone have any suggestions? Of course, one option
> is to simply put a harmonic bond between the two atoms, but this is
> quite coarse and not preferred. I would also like to avoid trying
> to manually change the psf.
>
>
> Thank you,
> Jim
>