Easiest way will be to just open the npt/nvt/em file using text editor and see which atom is present at position 1399 and it will also indicate the name of Residue with residue position in sequence.

Analyzing the MD data with chimera is more easy compared to VMD, as residue position and atomic information is displayed by just clicking on the atom. Although, VMD has more options of post MD analysis.

Hope it helps..

regards

Tanuj

1. Upload your PSF and DCD files into the VMD.

2. Click on Graphics and select Representations.

3. Type the keyword "resid 1399 and not water" in Selected Atoms

4. Press enter

5. In Coloring Method choose ColorID red in adjacent tab

6. In Drawing Method choose Licorice

7. Now you can see your selected residue number in VMD OpenGL Display

8. Now press 1 in your keyboard and click on that selected residue number

9. Now you can see the residue name of your selected residue number.

Hope you will get the information which you want to know.

Thanks

I think Varun has answered it the best if you want to know the specific amino acid for that particular residue number. Also, visually it gives you much more information. However, if you want to know it quickly and programmatically, use MDAnalysis. Here is the basic code.

import MDAnalysis as mda

u = mda.Universe(PSF, DCD)

print(u.atoms.select_atoms('resid 1399').resnames)