AW: Re: [gmx-users] where can I download POPC membrane file?

[Thomas Piggot]

In addition to all the other responses, I just wanted to clear up why
there is this difference in names. The POPC structure from the link
below still has the atom names of the old CHARMM27 lipids (DPPC is
fine). As suggested, a simple script can do the conversion for you.

Cheers

Tom

albert wrote:
> I know this, but this file cannot be used because the atom name is quite 
> different from gromacs CHARMM36 topol library.
> 
> 
> At 2011-05-30，"Rausch, Felix" <frausch at ipb-halle.de> wrote:
> 
>     Check this link given by another (unknown) mailing list user
>     yesterday (Topic name: *about POPC in Gromacs* )!
>      
>     http://terpconnect.umd.edu/~jbklauda/research/download.html
>     <http://terpconnect.umd.edu/%7Ejbklauda/research/download.html>
> 
>     ------------------------------------------------------------------------
>     *Von:* gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org> im Auftrag von albert
>     *Gesendet:* So 29.05.2011 21:23
>     *An:* Discussion list for GROMACS users
>     *Betreff:* Re:Re: [gmx-users] where can I download POPC membrane file?
> 
>     But I don't think it is pre-equilibrium POPC membrane...... and more
>     over, the position from VMD is not pre-aligned with OPM database. It
>     would be a great problem for putting our protein in the membrane......
> 
> 
> 
> 
>     At 2011-05-30，"Sergio Manzetti" <sergio.manzetti at vestforsk.no
>     <mailto:sergio.manzetti at vestforsk.no>> wrote:
> 
>         You can build it using VMD (VIsual Molecular Dynamics)
> 
> 
> 
>         2011/5/30 albert <leuven at yeah.net <mailto:leuven at yeah.net>>
> 
>             Dear all:
> 
>               I would like to use charmm36 and POPC for membrane protein
>             simulation. and I am wondering where can I download charmm36
>             pre-pribriumed POPC PDB and topol file for gromacs?
> 
>             Thank you very much
>             Best
> 
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> 

-- 
Dr Thomas Piggot
University of Southampton, UK.