VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Sep 19 2006 - 10:43:53 CDT

Does your pdb have the bond before you run psfgen? And do you load
the psf and then load the pdb into VMD? Also, which bond is missing?

I expect any more information you could provide would be helpful in
this case.

On Sep 18, 2006, at 5:24 PM, Al-Rawi, Ahlam wrote:

>
> Dear All,
> I am preparing a psf for a Beta sheet protein that start with NH3
> then KKK and at the end it has KKK and (C=O NH2)
> The results pdb file has a missing bond and I have no idea why??
> In the topology file :
>
> **I added the NH3 to the first LYS after removing the NH and then I
> call it AHS
> **and I renamed the last LYS to ASE after removing the C=O
> **The last molecules I add it as a new residue contain(C=O and NH2)
> I need to know why I have the missing bond when I view the pdb file
> in vmd.
> Thanks,
> Ahlam
> Ahlam Al-Rawi
> Physics Department
> Kansas State University
> 785-532-5520
> cell 785-317-5858
>