Rebeca García Fandiño wrote:
Hello,
I would like to transform to pdb a .gro file I have obtained from an
equilibration in Gromacs. I have tried directly with editconf:
editconf -f equilibrated.gro -o equilibrated.pdb
but the lipids of my membrane appear divided due to PBC.
Then I have tried:
editconf -f equilibrated.gro -o equilibrated.pdb -pbc
and they don´t divide, but the membrane and protein are in a side and
the water and ions in the other side. They are not where they should be.
How could I convert a .gro file to a .pdb with no PBC and in the right
place, like the output file of a NAMD or AMBER program?
If you're correcting for PBC, the best tool is trjconv. Explore the -pbc and
-center options to compensate for periodicity.
-Justin
Thank you very much for your help in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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