[gmx-users] question about all atoms lipid molecule structure and force field

[Justin A. Lemkul]

Amit Choubey wrote:
> Thank you,
> 
> Is it really necessary for me to use Charmm FF for all atom calculations 
> on lipids? 
> 

You can use whatever model you want, provided it's valid.  Just so happens that 
most people who use all-atom models of lipids use CHARMM.

> The reason I am asking this is because it will require me to create 
> gromacs compatible FF files of the Charmm FF . I did find two perl 
> scripts which can do probably handle that but i am wondering if the 
> compatible FF are already up on gromacs website somewhere.
> 

No one ever said life was easy :)  CHARMM support is under development, you can 
get the source via the git repositories, but I don't know its current status.

-Justin

> 
> amit
> 
> 
> 2009/10/14 LuLanyuan <lulanyuan at msn.com <mailto:lulanyuan at msn.com>>
> 
>     Hi,
>     You can find some configurations here:
>     http://persweb.wabash.edu/facstaff/fellers/
>     And I think you can use Charmm FF.
>     Lanyuan
> 
>     ------------------------------------------------------------------------
>     Date: Wed, 14 Oct 2009 11:29:26 -0700
>     From: kgp.amit at gmail.com <mailto:kgp.amit at gmail.com>
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Subject: [gmx-users] question about all atoms lipid molecule
>     structure and force field
> 
> 
>     Dear all,
> 
>     I have been trying to search for an all atom DPPC sructure
>     (including the missing Hydrogens of long chain hydrocarbons) and
>     then do an all atoms md simulation on it. I havent yet found any
>     such structure or any force field that could be used for it on the
>     internet. Is anybody familiar with any such work ?
> 
>     Is there any all atom model for hydrocarbons which is incorporated
>     in Gromacs? I am not 100 % sure about it.
> 
>     I want to do this to parametrize another force field which
>     essentially uses all atom model.
> 
>     Thank you,
>     Amit
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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