[gmx-users] Berger lipid

[Shima Arasteh]

Dear Thomas,
It's a good idea. Thanks :)

 
Sincerely,
Shima


----- Original Message -----
From: Thomas Piggot <t.piggot at soton.ac.uk>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Friday, June 29, 2012 1:39 PM
Subject: Re: [gmx-users] Berger lipid

Hi Shima,

The lipids.rtp file in the charmm36.ff folder has many different entries for lipids. All you need to do is to run pdb2gmx with just one of your lipids of interest. This will produce a .top for this one lipid which is trivial to convert into an .itp (see Chapter 5 of the manual).

Cheers

Tom

Peter Lai wrote:
> 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

-- Dr Thomas Piggot
University of Southampton, UK.
-- 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