[gmx-users] protein membrane simulation

[maite lopez]

Hi Tsjerk:

Of course, i was wrong,  the force field i said is  ffG45a4, not  43a4.
In the article: A Biomolecular Force Field Based on the Free Enthalpy
of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5
and 53A6. (2004)  Ostenbrink et al. refers that:
" The recent parameterization efforts regarding the description of
sugars, nucleotides, and lipids have resulted in the definition
of a parameter set called 45A4. "

But , it isn't implemented in gromacs 3.3.

Thanks a lot, I'll use  ffG45a3.

Maite



On 4/5/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
Hi Maite,
>
> You can use ffG45a3, which is an upgrade of ffG43a2; I've never heard
> of 43a4, but that's probably me. 45a3 and 43a2 are largely similar and
> AFAIK you don't need to renumber bonded interactions and such.
>
> Best,
>
> Tsjerk
>
> On 4/5/07, maite lopez <lopezmai at gmail.com> wrote:
> > Hi all:
> >
> > Thanks a lot for replyng.  You 're right, i include the popc.itp file
> > in my .top and grompp runs well.  I've changed to ffG43a2 force field,
> > as David and Tsjerk said me, the ffG53a* isn't a good force field for
> > lipids. The best of the gromos96 ff is ffG43a4 for membrane
> > simulations,  but gromacs 3.3 hasn't it.
> >
> > Chris, i found that  ffG43a2 requires the same valor of FudgeQQ than
> > the Berger lipids. I don't have to do this transformation. Thanks for
> > the last email. I could to mix the Berge and GROMOS96 force field
> > following your steps.
> >
> > if somebody have to do something similar don't forget to change the
> > atoms OW1 x OW, HW2 x HW1 and HW3 x HW2  in the membrane.gro file.
> > Grompp gives these warnings:
> >
> > Warning: atom names in membrane.top and membrane.gro don't match (OW - OW1)
> > Warning: atom names in membrane.top and membrane.gro don't match (HW1 - HW2)
> > .....
> >
> > Cheers,
> >
> > Maite
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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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