[gmx-users] how to make top and gro file for acid hexanoic

[Justin A. Lemkul]

cuong nguyen wrote:
> Dear,
> 
> I have used JME in PRODRG to draw acid hexanoic molocule. However, after 
> running, the H atom in -OH could not be created and two oxygen atom were 
> the same.
> 
> Please tell me what are the errors?
> 

Please read the PRODRG FAQ's, where protonation state is addressed.

-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

========================================