[gmx-users] Protein Solvent Dynamics - Coordinates for docking

ram bio rmbio861 at gmail.com
Wed Oct 21 13:07:36 CEST 2009

Dear Gromacs Users,

I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt  md_0_1.edr  md_0_1.gro  md_0_1.log
md_0_1.tpr  md_0_1.trr  md_0_1.xtc. I am following Justin Tutorial.

Can anybody tell me how to extract the coordinates ? of the simulated
protein (file after extraction ?) and is it necessary to minimize the
simulated protein in vacco to use it for further docking studies.

Please help.



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