g...@bioacademy.gr wrote:
Hello
Given that the partial charges from PRODRG are not reliable (as explained
Justin Lemkul's paper),
are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable
starting point?
Yes, those charges are a reasonable start, but will almost certainly not be
sufficient for the final topology.
In this case, do we treat all ligand atoms as one charge group?
Unless your ligand is 4 atoms or less, no. Please consult the manual regarding
charge groups, and see existing Gromos96 building blocks for suitable charge
groupings.
-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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