[gmx-users] protein membrane simulation
lopezmai at gmail.com
Fri Apr 6 00:07:39 CEST 2007
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.
On 4/5/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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.
> 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
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> The Netherlands
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