[gmx-users] PRODRG charges

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 21 19:30:58 CET 2011

gpat at 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 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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