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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