[gmx-users] question about all atoms lipid molecule

[Amit Choubey]

Hi Par Bjelkmar,

I need to do an all atom simulation for dppc bilayer . You are right the
dppc molecule file that i have has PALM and PCGL residues.

I will like to try to set up the charmm FF for gromacs. But I dont have the
FF files with me, neither do i have the programs. Could you send me a
tutorial or some reference link too ( if you know of any).

Thank you,
Amit







On Thu, Oct 15, 2009 at 4:01 AM, Pär Bjelkmar <bjelkmar at cbr.su.se> wrote:

> Hi,
>
> 15 okt 2009 kl. 07.08 skrev gmx-users-request at gromacs.org:
>
>
> 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, it is not available on the gromacs website yet. You can get the current
> parameter files from me if you'd like to try it out. I'm afraid the DPPC
> lipid in CHARMM is created by combining the PALM and PCGL residues and some
> patches so if you know how that works in CHARMM you might be able to create
> the DPPC residue.
>
>
>
> 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.
>
> As Justin is saying, CHARMM will be supported as of version 4.1. The source
> code is there in git master branch but you need to get the ff files from
> me.
>
>
>    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.
>
>
> /Pär Bjelkmar
>
>
>
> <><><><><><><><><><><><><><><><><><>
>
> Pär Bjelkmar, PhD student
>
>
> Stockholm Center for Biomembrane Research,
>
> Stockholm Bioinformatics Center,
>
> Department of Biochemistry and Biophysics,
>
> Stockholm University
>
>
> Tel:  +46-8-16 2746
>
> Fax: +46-8-15 3679
>
> E-mail: bjelkmar at cbr.su.se
>
> Home: http://www.dbb.su.se/User:Bjelkmar
>
> <><><><><><><><><><><><><><><><><><>
>
>
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