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?
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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