[gmx-users] Berger lipid

[Shima Arasteh]

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

========================================


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