From: Song, Hyundeok (songhk) (songhk_at_mail.uc.edu)
Date: Mon Dec 28 2009 - 10:03:38 CST
I got dmpc.pdb from http://bioinfo.mol.uj.edu.pl/modmol/PiotrLiguzinski
And I used the same method to build dmpc bilayer as http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
I hope this is helpful.
Hyun.
________________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Axel Kohlmeyer [akohlmey_at_gmail.com]
Sent: Monday, December 28, 2009 3:59 AM
To: Syed Kashif Zafar
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: dmpc bilayer
On Sun, Dec 27, 2009 at 4:10 PM, Syed Kashif Zafar
<skashifzafar_at_yahoo.com> wrote:
>
> hi all,
> I am new in namd. i completed membrane protein tutorial.now i want to build dmpc bilayer on membrane builder but it has only two bilayer.POPC and POPE.i also read namd mailiing list but i am confused.
the membrane builder is a VMD plugin, so it would be advisable to also
search through the VMD mailing list for useful information. in order to get
more adequate help (and to avoid guessing) it would be extremely helpful,
if you would have stated _what_ is confusing you. i also strongly advise to
first practice using NAMD on a simpler system, since managing a bilayer
+ protein + water system _and_ learning how to use NAMD properly can be
very difficult and more confusing. you have to keep in mind that the tutorials
are designed to work well. typical systems don't work that well and require
some experience in the various options of the simulation package you are
using to be able to tell what is working or going wrong.
> if anyone guide me so it is highly appreciable.
the membrane builder indeed only comes with two preequilibrated membrane
templates, POPC and POPE, but you can supply your own as well. if memory
serves me well, the corresponding .psf/.pdb files for pre-equilibrated bilayers
using other lipids can be downloaded from locations on the web.
cheers,
axel.
> thanx in advance
>
>
>
> SYED KASHIF ZAFAR
> JUNIOR RESEARCH FELLOW
> H.E.J Research Institute
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:38 CST