Yes, I know that as studied the Kalp15 tutorial. Sorry, the last question :) :
DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is it ok? Because I see that POPC.itp is also required for simulation of protein in bilayer. Again, thanks Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, June 29, 2012 5:16 AM Subject: Re: [gmx-users] Berger lipid On 6/28/12 8:43 PM, Shima Arasteh wrote: > > > Yes, I have studied the article by Jeffery B. Klauda and other articles > related to C36. And know where the parameters of CHARMM36 were derived. > > By the way, when I search the lipidbook to find the .itp file I can't find > it! What about the lipid .itp ? Is it required yet? ( in your tutorial it's > written "lipid.itp - Berger lipid parameters" ) > You do not need the so-called "lipid.itp" as it is for a completely different force field. The "Berger lipids" are a united-atom parameter set derived in 1997 from a hybrid of OPLS and Gromos parameters. They are typically combined with Gromos force fields. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
