Biomodeling: Analysis and Visualization
Intro
Download link: https://www.dropbox.com/scl/fo/793kcxhjhj7q7ye5sh51y/h?rlkey=1rrx9y0h1iuzc7suh2q15sfbq&dl=0
Download trjconv and vmd folders
References
A case of membrane channel protein
In trjconv/conf.pdb, you can find a system with a tetrameric membrane channel embedded in a lipid bilayer.
gmx mdrun will generate trajectory files, such as traj_comp.part0001.xtc.
An example is uploaded as traj_comp.part0001.xtc
Loading traj_comp.part0001.xtc to VMD will show a messy conformation.
Post-processing the XTC files is useful for analysis and visualization.
Initial conformation in conf.pdb
traj_comp.part0001.xtc
A shell script for post-processing XTC outputs.
#!/bin/bash
for i in traj_comp.part????.xtc # initial XTC files with 20 ps time step.
do
o=$(echo $i | sed "s/.xtc/.1ns.xtc/")
if [ $i -nt $o ]
then
echo "Protein 0" | gmx trjconv -s topol.tpr -f $i -o $o -pbc mol -ur compact -center -skip 50
fi
done
rm -f all*xtc
echo 0 | gmx trjcat -f traj_comp.part????.1ns.xtc -o all.1ns.xtc #-cat
rm -f *tmp* *#*
How to handle protein or DNA complexes.
gmx trjconv can make a molecular structure whole based on chemical bonds.
Thus, gmx trjconv can make each molecule whole individually, not as a complex.
For multimeric complexes such as dsDNA and channel proteins, having non-physical bonds can be useful.
gmx pdb2gmx .... -merge all
This will generate a single moleculetype definition including all.
prot2enm.pl
This Perl script will generate bonds.
Paper quality graphics and movies using VMD
In vmd folder, you can find VMD.pdf and sample files.