Hi Albert,
I'll add to this that the force field is effectively your choice. E.g. you can take the pdb from the Charmm Lipid builder and run it through Leap to use the AMBER Lipid 14 force field if you want.
See: http://ambermd.org/tutorials/advanced/tutorial16/index.html
All the best
Ross
> On Aug 2, 2016, at 9:17 AM, Amy Rice <arice3.hawk.iit.edu> wrote:
>
> 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 - 09:30:03 PDT
