[gmx-users] packing lipid around protein

Balasubramanian Suriyanarayanan bsnsuri at gmail.com
Tue Jun 10 15:22:50 CEST 2014


thanks a lot


On Tue, Jun 10, 2014 at 3:26 PM, Catarina Santos <catsantos at itqb.unl.pt>
wrote:

> Dear Balasubramanian,
>
> If you are using inflategro, you have to manually update the number of
> lipid molecules in your system topology (if the perl script does not output
> the number of lipid molecules that were removed, just count the number of
> lipids before and after the lipid removal step).
>
> If you are using inflategro2 (which is better in several ways: link
> <http://pubs.acs.org/doi/abs/10.1021/ci3000453>), the perl script will do
> this automatically and output the number of lipids removed from each
> leaflet.
>
> Kind regards.
>
> Catarina A. Carvalheda dos Santos
>
>
> On 10 June 2014 08:49, Balasubramanian Suriyanarayanan <bsnsuri at gmail.com>
> wrote:
>
> > Dear Friends
> >
> >  When I pack the lipids around the protein using the command
> >  "perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5
> area.dat",
> >
> > how do we know how many lipids are lost?
> >
> > regards
> > Suriyanarayanan
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>
>
> --
>
> Catarina A. Carvalheda dos Santos
> Research Student
> Molecular Simulation Laboratory
> Instituto de Tecnologia Química e Biológica
> Universidade Nova de Lisboa
> Av. da República, Estação Agronómica Nacional
> 2781-901 Oeiras, Portugal
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