[gmx-users] PRODRG charges

[Justin A. Lemkul]

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 
groupings.

-Justin

-- 
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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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