From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Sat Apr 09 2005 - 07:20:07 CDT
Dear Baoqiang,
We have developed a package for that purpose. The package is able to build the
whole system (membrane+protein+solvent) with the advantage that every
pair of atom of different molecules keep safe distances. This package
will build a pdb file for you from which you can run psfgen to build
the psf file.
The package is available at
http://www.ime.unicamp.br/~martinez/packmol
Get the new beta-version, which is able to build those kind of system.
This version is already ready, but it is still as beta because we are
writing a new site.
Best regards,
Leandro.
On Apr 8, 2005 12:02 PM, Baoqiang Cao <caobg_at_email.uc.edu> wrote:
> Dear All,
>
> I'd like to build a system consists of membrane, membrane protein, and solvent. Following some tutorials, I have got a membrane by run "membrane -l popc -x 60 -y 60" on VMD, it is away from the protein. It is really hard to graphically position the protein in the membrane, especially considering an old monitor and a very obsolete CPU. A script beening able to build the whole system and then psf and pdb files for MD is highly appreciated, any helps please? Thanks.
>
> Best,
> Baoqiang Cao
>
>
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