[gmx-users] packing lipid around protein

Catarina Santos catsantos at itqb.unl.pt
Tue Jun 10 11:56:46 CEST 2014

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

Kind regards.

Catarina A. Carvalheda dos Santos

On 10 June 2014 08:49, Balasubramanian Suriyanarayanan <bsnsuri at gmail.com>

> 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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