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

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 3 02:41:51 CET 2011

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 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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