[gmx-users] using .pdb file from protein data bank

Madhuri Agashe magashe at CLEMSON.EDU
Thu Jan 15 19:05:01 CET 2004

I want to use a pdb file from the protein data bank and run a MD simulation
on it.

How does gromacs treat the pdb file taken directly from the protein data
bank? Are protonation sites checked or protonation/deprotonation done?

How can I check the total charge on the protein before starting the

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