[gmx-users] Re: how to write the correct top file for membrane protein

liang petrucci123 at vip.sina.com
Tue Nov 27 15:10:00 CET 2007

Hi Mark,

i indeed checked some publications about how to choose lipid force field,
please check this reference: Journal of Physics: Condensed Matter 18(2006) 
Tieleman and his coworkers tested two combinations: Berger+ffgmx+SPC, 
and  they recommended that using OPLS together with united-atom lipid force 
So, i would like to know whether it is reasonable or not, and how should i 
modify them in top file?

Thanks for your reply.


----- Original Message ----- 
From: <gmx-users-request at gromacs.org>
To: <gmx-users at gromacs.org>
Sent: Monday, November 26, 2007 5:28 PM
Subject: gmx-users Digest, Vol 43, Issue 96

> Message: 4
> Date: Mon, 26 Nov 2007 12:24:31 +0800
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: how to write the correct top file for
> membrane protein
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <474A4A7F.3060100 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> liang wrote:
>> Dear Mark,
>> Thanks for your advice, but from my understanding, Berger's force field
>> is based on OPLS/Amber.
>> Lipid itp files from Tieleman's website just use the atom type
>> definitions from GROMOS87.
>> And GROMOS87 is out of fashion now.
>> So thats why i think it would be better to use OPLS for protein and
>> "ffgmx.itp" for lipid.
> Fine, but you can't use them both at the same time (unless you want to
> produce indefensible gibberish), and ffgmx is deprecated anyway.
>> I am not sure whether I misunderstand the usage of Berger's force field,
>> if i am wrong,
>> please give me further instruction.
> See my advice last time.
>>> Don't mix forcefields unless you already have hard evidence that this
>>> combination works - and I'm not aware of any. The link Justin provided
>>> warns you about that. You need to find a force field that has parameters
>>> optimized that suit your system. Mixing anything else is about 99% 
>>> likely
>>> to make an expensive (and poor) random number generator.
> Look in the literature for systems similar to yours and see if their
> ideas on force fields are suitable for you to use. Making it up based on
> stuff you found on the web is for high school students doing assignments 
> :-)
> Mark

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