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

Mark Abraham 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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