[gmx-users] on Umbrella Sampling
Justin A. Lemkul
jalemkul at vt.edu
Sun Apr 1 15:13:54 CEST 2012
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.
> *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
> > Can you give me further clarification?
> The .gro file is renumbered during pdb2gmx.
> -- ========================================
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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