[gmx-users] generation of acetic acid protonated .itp file

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 14 12:36:48 CEST 2011

Sunita Patel wrote:
> Dear gmx-users,
> I am trying to build acetic acid protonated form using PRODRG to run a
> simulation using GROMOS96 forcefield. The information says it can only build
> acetate ion but not the protonated form of acetic acid. 
> How can I build acetic acid (protonated form) .itp file compatible to GROMOS96
> forcefield.  

See the PRODRG FAQ's.  Protonation state is addressed there.  Be sure to 
re-assign the charges that you get from PRODRG.


> Your help will be appreciated.
> Best regards,
> Dr. Sunita Patel
> ---------------------------------------------
> Visiting Fellow
> Department of Chemical Sciences
> T.I.F.R., Homi Bhabha Road, Colaba
> Mumbai - 400005
> ---------------------------------------------


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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