Dear Peter, Thanks a lot :) Sincerely, Shima
----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, June 29, 2012 2:54 PM Subject: Re: [gmx-users] Berger lipid yes http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract The files are here: http://uab.hyperfine.info/~pcl/files/popc36/ On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote: > 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 <p...@uab.edu> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
