AMBER Archive (2007)

Subject: Re: AMBER: membrane simulation

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Thu Apr 19 2007 - 07:51:56 CDT

Dear Vlad Cojocaru ,
                                      Thank you for your suggestions.
                            
                                                      with regards,
                                                    nagaraju mulpuri.
Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
  Dear Nag,

You could try to do the same as Balazs and Tamas did with POPC membranes (use the gaff force field via antechamber and RESP charge derivation). Of course you would need to test the procedure carefully for DOPC. An alternative is to look back at some older united atom ff for DOPC. Such parameters are described for POPC by Jung-Hsin Lin, N. Baker, and Andy McCammon in the Biohysical Journal (2002). You could in principle use the same methodology as they did to derive parms for DOPC. Of course, extensive testing needed ....

This, if you want AMBER parameters ....

I certainly hope that future versions of AMBER will come with parameters for diverse lipids. It is something that AMBER still lacks comparing to other force fields. However, the gaff ff might be a good starting point ..

Cheers
vlad

nag raj wrote:
Dear Amber users, Can you help me in getting parameters for DOPC lipid bilayer. Any suggestions is appriciated. Thank you in advance, with regards, Mulpuri. --- Florian Haberl <Florian.Haberl_at_chemie.uni-erlangen.de> wrote:
  
Dear Balazs Jojart & Tamas A. Martinek, On Sunday, 15. April 2007 20:06, Jojart Balazs wrote:
  
Dear Amber users, we've tested the GAFF performance in fully

hidrated lipid bilayer
  
simulations. As David A. Case suggested, we would

like to share our
  
experinece. The article is available:

http://www3.interscience.wiley.com/cgi-bin/abstract/114209721/ABSTRACT.
    
We hope that out results help to everybody, who

would like to simulate
  
membrane bilayers.

are you planning to release pre equilibrated structures of your membrans on the web, like Tielman has done for gromos based membrans? (link:

http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
  
      
  
Balazs Jojart & Tamas A. Martinek Unversity of Szeged

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majordomo_at_scripps.edu Greetings, Florian --

-------------------------------------------------------------------------------
  
 Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de

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-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533266 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------

       
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