[gmx-users] on Umbrella Sampling
acootbrett at yahoo.com
Sun Apr 1 15:11:39 CEST 2012
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?
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:
> 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 A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
-- gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users