I used VMD to determine the exposed residues of proteins, however, it does not say which residue is of particular amino acid is exposed or buried.
Dear Narendra, VMD is a poor software for this. you can use a VADAR (Volume, Area, Dihedral Angle Reporter) for determination of this parameter. This software display some parameter that can help you.
Best regards
If you have SPDBV (Swiss PDB viewer) then it is very easy. Do as following.
1. Browse Your PDB file >> Select >> Accessible Residue....It will open a new widget asking >= % accessibility of Residues by solvent...Select your range >> OK
2. Color >> By Selection. This will display the Solvent Accessible Residues if any under your selected range. If not then reduce down your % accessible range.
The default value is 30%. Also you can do the same directly with default value by
3. Select >> All. Color >> Accessibility
The dark blue residues displayed are buried one on the other hand light green to green are surface exposed accessible.
You can also save the surface residues by
4. Select >> Accessible Residue
File >> Save >> Selected residues of Current Layer.
Enjoy.
- Badges
- Science topic
- Similar topics
- Chemistry
- Pharmacology