[gmx-users] protein membrane simulation

[Tsjerk Wassenaar]

Hi Maite,

Actually, that 45a4 is just a minor upgrade from 45a3, mainly
formalizing some additions which I think are already available in 45a3
as present in Gromacs (but who needs nucleotides anyway ;)).

Best,

Tsjerk

On 4/6/07, maite lopez <lopezmai at gmail.com> wrote:
> 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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-- 
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