[gmx-users] protein membrane simulation
tsjerkw at gmail.com
Thu Apr 5 20:53:00 CEST 2007
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)
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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