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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
========================================
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