[gmx-users] on Umbrella Sampling

[Justin A. Lemkul]

Acoot Brett wrote:
> I have not read your original article. Maybe I will read it tomorrow. 
>  
> But the original pdb file has 5 same chains, and from your tutorial it 
> seems you pdb file for the tutorial has 2 different chains. Will you 
> please let me know how do you get you pdb file for your tutorial/ Or you 
> just have 1 chain in your tutorial PDB file, but in the gro file you 
> defined it into 2 chains from a single chain?
>  

The structure has 5 chains.  The purpose was to calculate the binding free 
energy for the terminal peptide (chain A) to the complete structure (i.e., 
interacting with chain B).  The rationale for restraining chain B is explained 
in the article.

-Justin

> Cheers,
>  
> Acoot
> 
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Sunday, 1 April 2012 11:04 PM
> *Subject:* Re: [gmx-users] on Umbrella Sampling
> 
> 
> 
> Acoot Brett wrote:
>  > Thanks.
>  >  The original PDB file (2BEG) has 5 chains. In your tutorial you fix 
> chain B. Thus if I am right, the energy calculated should be the 
> disintegation energy of the whole protein to the 5 chain peptide. In 
> addition the protein chain in the original pdb is from residue 17 to 42.
>  >  This makes me confused when you define "1-27" to chain A, and 
> "28-54" to chain B.
>  >  It seems your tutorial protein is a 2 chain protein, not the 5 chain 
> protein.
>  >  Can you give me further clarification?
>  > 
> 
> The .gro file is renumbered during pdb2gmx.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================