[gmx-users] Berger lipid

[Christopher Neale]

I am sure that a lot of this could be avoided if the gromacs users-list search feature worked. 
Every search that I do returns ten to one hundred versions of each hit, making it nearly unusable.
Google is ok, but it doesn't search the gromacs list nearly as well as the old specific search on the
gromacs website did before the website changes.

Given the current state of the list search feature, it's not really feasible to ask people to search first, unfortunately.

Chris.

-- original message --


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