Chunxia Gao wrote:
Dear Justin:

What I mean is can I calculate the free energy of restraining the ligand in the 
binding site, since I put on distance restraint to the ligand and the protein?


Ah, now I see. I'm not sure, but I know the answer is out in the literature somewhere; various types of restraints are implemented in free energy calculations fairly routinely.

-Justin

Regards
Chunxia

Chunxia Gao wrote:
Dear Justin,

If I apply the pull code to the distance restraints, can I calculate the free 
energy of those restraints through g_bar? In what way?


The pull code and free energy code are independent.  I see no reason why you
could not proceed in the same manner as the free energy tutorial describes, but
with the addition of your restraint.

and the pull code can only be applied to distance restraints, right? not angle 
or dihedral restraints?


Correct.

-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

========================================



--
========================================

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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