[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

[Justin A. Lemkul]

Please do not include the entire digest in your post.  The archive becomes 
hopelessly confusing when this happens...

arun kumar wrote:
> hi justin,
> 
> as u said i understand that there is inconsistency in the charges and 
> charge groups of  PRODRG server itself.
> can u suggest me any other softwares that i can rely on for this work.
> 

Yes, ATB is one option, or you can modify the PRODRG topology after doing your 
own charge calculations, as described in 
http://pubs.acs.org/doi/abs/10.1021/ci100335w.

-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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