Dear Colleagues,
We have performed MD for RMSD and RMSF calculation of Ligand-protein complex using NAMD/VMD. Now, one reviewer is insisting us to also calculate RMSD and RMSF of Ligand only.
Is there a way to extract RMSD and RMSF of Ligand only from a .dcd file or through a separate MD?
I have tried RSMD calculator of VMD after opening the psf,pdb and dcd file but "atom selection" is giving error. I wrote UNK and/or LIG ETC. as per psf file but none worked...
Many thanks in advance
Open the VMD ->Extensions->RMSD Trajectory tool -> resname UNK or LIG measure RMSD
another approach check the resid of the protein and ligand. suppose ligand resid is 100 and protein resid 1 to 99.
Type in VMD resid 100, then measures RMSD.
Then you can easily able to calculate the RMSD of Protein and Ligand separated.
Try this tool:
https://ligrmsd.appsbio.utalca.cl/
But be aware of a bug, drag twice your coordinate file the first time.
Good luck
Hello,
We know RMSD plugin in VMD is here https://www.ks.uiuc.edu/Research/vmd/plugins/rmsd/
for RMSD there may be a reason why you got the wrong data:
1. Selection for example resname/segname or other selection, you may check when you load the structure in VMD and then go to Graphics > Representation > Selection
- then choose either resname or segname or other selection and see what is their name or type mentioned
- go back to rmsd window and make selection accordingly.
For example: you see segname XYZ, then go to the rmsd trajectory window and yo can make a selection segname XYZ; or can be more creative by changing the selection to segname by selecting as segname ABC.
2. Tyring to check the vmd mailing list will be a great resource, other websites and VMD tutorials can be good idea to follow: https://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/node7.html
Also, you can see researchgate earlier discussion:
https://www.researchgate.net/post/How-can-I-calculate-RMSD-per-residue-of-a-protein-in-VMD
These can be helpful
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