From: JC Gumbart (
Date: Wed Sep 20 2006 - 14:43:38 CDT

I am not sure why you are renaming the residues, or making them
different numbers. What you want, I think, are actually just
standard types of termini. Without any modification of the pdb
necessary (no deleting atoms, renumbering, etc.), you should be able
to define your segment something like this:

segment A {
first NTER
last CT2
pdb beta.pdb

and then after the rest of your commands, it should come out fine.

Look at the definitions in the topology file for more information;
also the psfgen user's manual has good tips:

Let us know if that does what you want.

On Sep 19, 2006, at 12:03 PM, Al-Rawi, Ahlam wrote:

> I atached my pdb files,beta1.pdb is the original file beta.pdb the
> one that I chang.
> Yes it has the bond and I did change this pdb file so that RESI(0)
> +RESI(1) become RESI AHS
> The missing bound is between RESI (AHS) AND RESI (LYS 2) and LYS(10)
> and (AHE).
> I need to know how I let the topology file think that AHS and AHE
> is conected to the rest.
> Thanks
> Ahlam
> Ahlam Al-Rawi
> Physics Department
> Kansas State University
> 785-532-5520
> cell 785-317-5858
> -----Original Message-----
> From: JC Gumbart []
> Sent: Tue 9/19/2006 10:43 AM
> To: Al-Rawi, Ahlam
> Cc:
> Subject: Re: vmd-l: psf for protein
> 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
> <beta1.pdb>