[gmx-users] Protein Solvent Dynamics - Coordinates for docking
Mark.Abraham at anu.edu.au
Wed Oct 21 13:12:46 CEST 2009
ram bio wrote:
> 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
It sounds like you should be doing more tutorials to understand GROMACS
workflows better. What coordinates you produced are in the .trr or .xtc
files, but what data is there with what frequency is set up in your .mdp
file, so you need to plan that in advance. trjconv is the tool for
manipulating those files, for example to extract frames as PDB to use
with some other software.
> simulated protein in vacco to use it for further docking studies.
Maybe. Read the docking literature, or do some tutorials there.
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