[gmx-users] Selection of force field

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 19 20:19:07 CEST 2009

Hi Anindita,

Proper carbohydrate parameters were introduced in G45a3. But you're
not easily satisfied, wanting proteins carbohydrates and lipids to
work together! You're short of wanting to include nucleic acids :)
Anyway, the lipids are a bit problematic. There are parameters for
some lipids for the 53xx force fields (that also include the 45a3
carbohydrate parameters). Maybe it will help if you can be more
specific regarding the nature of the lipids.



On Tue, May 19, 2009 at 3:47 PM, ANINDITA GAYEN
<aninditagayen at yahoo.co.in> wrote:
> Dear all,
> I want to study "glycolipid-protein" interaction using united atom GROMACS
> force field. For lipid simulation we need lipid.itp, which is a mixture of
> lipid ( Berger) and GROMOS (ffgmxnb) parameters. From an earlier post in
> gmx-user list, i have come to know that “the ffgmx force field should not be
> used for production runs. To use popc in simulation, try to dig up popc
> parameters for a current force field (like ffG43a1)”.
> Now, as in FF.dat, ffG43a1 is the GROMOS96 force field and ffG43b1, ffG43a2,
> ffG45a3, ffG53a5 & ffG53a6 are the further modifications. For lipid-protein
> simulation, lots of people are shown to use ffG43a1 parameters. Now, my
> question is that, if ffG43a1 is better than the other ffG???? parameters? if
> not which one should be more appropriate for my glycolipid-protein system
> (containing sugar moiety)?
> Looking forward for any reply.
> thanks in advance,
> Ms. Anindita Gayen
> C/O Dr. Chaitali Mukhopadhyay
> Senior Research Fellow
> Department of Chemistry
> University of Calcutta
> 92, A. P. C. Road
> Kolkata-700 009
> India
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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