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

[albert]

Maybe you think it is a simple scrips, but for those fresh GROMACS user such as me, it would be a very difficult task.

Anyway, thanks a lot for the messages.




At 2011-06-01，"Thomas Piggot" <t.piggot at soton.ac.uk> wrote:

>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
>> 
>>             --
>>             gmx-users mailing list    gmx-users at gromacs.org
>>             <mailto:gmx-users at gromacs.org>
>>             http://lists.gromacs.org/mailman/listinfo/gmx-users
>>             Please search the archive at
>>             http://www.gromacs.org/Support/Mailing_Lists/Search before
>>             posting!
>>             Please don't post (un)subscribe requests to the list. Use the
>>             www interface or send it to gmx-users-request at gromacs.org
>>             <mailto:gmx-users-request at gromacs.org>.
>>             Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> 
>
>-- 
>Dr Thomas Piggot
>University of Southampton, UK.
>--
>gmx-users mailing list    gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110601/bf513f69/attachment.html>