VMD-L Mailing List

From: Al-Rawi, Ahlam (ahlam_at_phys.ksu.edu)
Date: Mon Sep 18 2006 - 17:24:27 CDT

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