[gmx-users] Converting united-atom topology to all-atom

[Semen Esilevsky]

Dear all,
I'm working with the lipids in the ffgmx ff, but we
also want to try an all-atom OPLS ff. 
The question is is it possible to obtain ready
all-atom topologies for DMPC and DOPC lipids? Probably
somebody knows the download place?
If not, what is the simplest way to convert united
atom topologies into all atom?

Thank you in advance,
Semen

--- "Nagy, Peter I." <PNAGY at UTNet.UToledo.Edu> wrote:
>  
> 
> 	-----Original Message----- 
> 	From: gmx-users-bounces at gromacs.org on behalf of
> Erik Lindahl 
> 	Sent: Wed 6/23/2004 4:57 AM 
> 	To: Discussion list for GROMACS users 
> 	Cc: 
> 	Subject: Re: [gmx-users] OPLS 1-4 interactions &
> intramolecular contributionsto interaction energies
> ...
> 	
> 	
> 
> 	Hi,
> 	
> 	> Can anybody tell me what the proper way of
> including
> 	> 1-4 non-bonded interactions with the OPLSAA FF is
> ?
> 	>> From previous messages in this list I gather
> that
> 	> there seems to be no unique definition and the
> scaling
> 	> factor for the 1-4 interactions including H-atoms
> seems
> 	> to be different in different Gromacs versions.
> What is
> 	> this factor in 3.2.1, what is it in 3.1.4 and
> which is the
> 	> "correct" one ?
> 	
> 	The scaling factors are defined in the force field
> files and not
> 	hardcoded. They have always been 0.5 for both
> charge and LJ in OPLS-AA,
> 	but other forcefields obviously have different
> serttings.
> 	
> 	For OPLS-AA you should include 1,4 interactions
> between hydrogen atoms,
> 	while many other forcefields prescribe you
> shouldn't (e.g. Gromos96).
> 	This is controlled with a standard flag to pdb2gmx,
> but the default
> 	value is set in the rtp file for the last couple of
> gromacs versions.
> 	
> 	
> 	Cheers,
> 	
> 	Erik
> 	
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