Hi Albert,
The following citations are provided on the CHARMM-gui website for the
membrane builder and lipid force fields used (I've just included a few of
them):
J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P.K. Eastman, J.A. Lemkul, S.
Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L.
Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im (2016). CHARMM-GUI
Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM
Simulations using the CHARMM36 Additive Force Field. J. Chem. Theory
Comput. 12:405-413 <http://dx.doi.org/10.1021/acs.jctc.5b00935>
J.B. Klauda, R.M. Venable, J.A. Freites, J.W. O’Connor, D.J. Tobias, C.
Mondragon-Ramirez, I. Vorobyov, A.D. MacKerell, Jr., and R. W. Pastor (2010)
Update of the CHARMM all-atom additive force field for lipids: Validation
on six lipid types J Phys Chem B. 114(23): 7830–7843
<
http://dx.doi.org/10.1002/jcc.21287>
R.M. Venable, A.J. Sodt, B. Rogaski, H. Rui, E. Hatcher, A.D. MacKerell,
Jr., R.W. Pastor, and J.B. Klauda. (2014)
CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of
Hydrogen Bonding and of Positive Curvature. Biophys J. 107(1):134-45
<
http://dx.doi.org/10.1016/j.bpj.2014.05.034>
You can see that these are references for CHARMM36 force fields. Also, all
the top/par files that the gui outputs have the naming convention
*_all36_*, which is another good hint.
I would recommend using chamber (within parmed) to convert the .psf and
.prm files to an amber compatible format; I believe the charmm-gui does
this for you in the last step but it might not hurt doing it yourself so
that you understand how the conversion works. For simulating your system,
you could use the .mdin files that the gui gives you to equilibrate the
structure, but you will want to think carefully about which ensemble to use
- NPT, NPAT, or NPgT. I personally prefer to write my own mdin files for
equilibration/production so that I know exactly which options I am using,
but the ones from charmm-gui give you a good place to start if you aren't
very familiar with Amber.
Hope this helps,
- Amy
On Tue, Aug 2, 2016 at 1:38 AM, Albert <mailmd2011.gmail.com> wrote:
> Hello:
>
> I built a membrane protein system from Charmm-GUI for Amber. I am just
> wondering does anybody have any idea which forcefield it is for this
> Amber system? Probably it already has been assigned with CHARMM36
> forcefield? And we can submit it to Amber for MD directly?
>
> Thank you very much
>
> regards
>
> Albert
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology
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Received on Tue Aug 02 2016 - 09:30:02 PDT
