Dear Peter, Is this article is the one you talked about? Beyond Modeling: All-Atom Olfactory Receptor Model Simulations Thanks in advance
Sincerely, Shima ----- Original Message ----- From: Peter Lai <p...@uab.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, June 29, 2012 7:14 AM Subject: RE: [gmx-users] Berger lipid Uh didn't we go through all of this like more than a month ago? I published a paper using C36 POPC and even a linked to my popc.itp for it on this list... Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly certain will result in an identical file... Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours. ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, June 28, 2012 7:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Berger lipid On 6/28/12 8:54 PM, Shima Arasteh wrote: > 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. > You need a topology of some sort. It depends on what parameters you have on hand. If you do not have popc.itp from anywhere, then you need to generate it somehow. If it is present in the .rtp file for CHARMM36 that you have, then you can run pdb2gmx on it. -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 -- 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
