[gmx-users] Berger lipid

[Shima Arasteh]

Dear Peter,
Thanks a lot :) 

 
Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 <pcl at uab.edu>
> To: Discussion list for GROMACS users <gmx-users at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at 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 at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
> -- 
> gmx-users mailing list    gmx-users at 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-request at 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
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================