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.
-Justin
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
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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