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: [email protected] [[email protected]] on behalf
of Justin A. Lemkul [[email protected]]
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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