AMBER Archive (2007)

Subject: Re: AMBER: membrane simulation

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Apr 19 2007 - 04:07:52 CDT

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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>
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>>>
>>>
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>>
>>
>>Greetings,
>>
>>Florian
>>
>>--
>>
>>
>>
>-------------------------------------------------------------------------------
>
>
>> Florian Haberl
>> Computer-Chemie-Centrum
>> Universitaet Erlangen/ Nuernberg
>> Naegelsbachstr 25
>> D-91052 Erlangen
>> Telephone: +49(0) â^' 9131 â^' 85 26581
>> Mailto: florian.haberl AT chemie.uni-erlangen.de
>>
>>
>>
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>
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-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
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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/

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