VMD-L Mailing List

From: Al-Rawi, Ahlam (ahlam_at_phys.ksu.edu)
Date: Wed Oct 18 2006 - 19:33:51 CDT

Dear All,
I have a system that contain anti-parallel beta-sheet in water.
I need to apply a force to separate the two parts of the beta-sheet.
I read the on-line instruction but still not very clear to me.
Your help always appreciated.
Thanks,
Ahlam

Ahlam Al-Rawi
Physics Department
Kansas State University
785-532-5520
cell 785-317-5858

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Al-Rawi, Ahlam
Sent: Tue 9/19/2006 12:03 PM
To: JC Gumbart
Cc: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: psf for protein
 
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 [mailto:gumbart_at_ks.uiuc.edu]
Sent: Tue 9/19/2006 10:43 AM
To: Al-Rawi, Ahlam
Cc: vmd-l_at_ks.uiuc.edu
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
>