i have a 10 ns simualtion of protein. I want to perform H bond analysis where I can get the number of H bonds that are form between residue number 10 - 50 in each frame. such that I get separate information about each residue in the same file.
any idea how can I do that. the gromacs pooled the total number of Hbonds in each frame.
Either create and index file for each residue and then use that one to create h-bond or you can also use CPPTRAJ to do this one. The command for CPPTRAJ is odd, so it is better to create a script that you can run.
Check this video for analyzing hydrogen dynamics in VMD:
https://www.youtube.com/watch?v=8gc6jzbImpc
or https://www.youtube.com/watch?v=XQYtks6sIrM
Actually you need this part of gromacs tutorial (http://www.mdtutorials.com/gmx/complex/09_analysis.html) and python library mdtraj (https://www.mdtraj.org/1.9.8.dev0/index.html)
# In gromacs
# create an index file with res 10-50 as a group
gmx make_ndx -f original.tpr -o index_res10-50.ndx
> r 10-50
> q
# create a TPR with only res 10-50
# edit your Protein ITP file and comment out everything except res 10-50
# edit your topol.top file and comment out everything except Protein under
[ molecules ]
# run 'gmx grompp' to create a TPR with only res 10-50
gmx grompp -f minimization.mdp -c equilibrated_system.gro -p topol.top -o res10-50.tpr
# extract only res 10-50 from the original production trajectory
gmx trjconv -f production.xtc -s original.tpr -o production_res10-50.xtc -pbc mol -n index_res10-50.ndx
> r_10-50
# run hbond calculation using res 10-50 TPR and XTC
gmx hbond -f production_res10-50.xtc -s res10-50.tpr ...
Hope this helps.
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