Yes, I remember now...................you are right :) But I didn't know the linked you sent me, was your own output! However I wanted to know if it is necessary to produce the .itp file on my own or not.
I still have this link, so will cite to you. It would be a good idea to see its package in lipidbook too. Thanks Peter Sincerely, Shima ________________________________ From: Peter Lai <[email protected]> To: Discussion list for GROMACS users <[email protected]> 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: [email protected] [[email protected]] on behalf of Justin A. Lemkul [[email protected]] 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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
