Hello,
I have ran MD simulation using NAMD and CHARMM36 forcefield and want to calculate RMSD values of each residues in a protein. Is there any tcl script that i can use in VMD?
I appreciate your valuable suggestions.
Thank you.
see:
https://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/node7.html , point 3
Hi Alvea! You need to have a pdb and/or xtc trajcetory containing only your protein. Then you open it with VMD, you choose there in Extensions Analysis and in Analysis you choose RMSD calculation. No additional script is needed.
Hey,
Both Annemarie Honegger and Inna Ermilova are right if your trajectory files are small enough to load into vmd.
However if your MD trajectory files are large enough (in the order of hunders of ns), probably then you need a script because of memory leak while loading these trajectory files. We always set the output trajectory files with certain number of steps for troubleshooting and physical memory issues.
The first script "rmsd.tcl" measures the rmsd depend on your selection. You can choose a single residue or the whole backbone with the "atomselect" command. Then you create a loop to calculate rmsd via "measure" command over all frames.
The bash script "exec" basically loading the trajectory files via executing the vmd and then releasing it to avoid memory leak in the process.
Also you can find useful scripts and tools in my website (www.alioacar.rf.gd)
Cheers,
Ali
Hi Ali! He does not need a script, he can convert the trajectory to smaller trajectories, if it is needed. VMD can process large enough files.
Hi again Inna,
Here are the numbers what I mean with small and large files. VMD is using 12 bytes of memory per-atom. That means a system containing 100,000 atoms need a 1.2MB memory of RAM per frame. If you want to load 10,000 frames then you need approximately 12 GB of physical memory and this is just for 10,000 frames. If you want to load 100,000 frames then you are out of physical memory. Concatenating trajectory files is another option bu it takes the same amount of time and I think it is not practical. Using these scripts also allow you to perform different analysis.
Thank you everyone for your valuable information.
Apart from asking the query, I continued to search for it simultaneously. And I came across a tcl script for rmsd for individual residues. Below is the link for the script that i found:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-19545/residue_rmsd.tcl
And also how to run the script is given in the link below:
https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node15.html#SECTION00061100000000000000
I think per residue deviation means calculating RMSF for which there are scripts available online. You can use the following link :
https://youtu.be/CkCREhk1SL4
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