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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