From: Arjun Sharma (arjunsharma83_at_gmail.com)
Date: Sat Mar 14 2015 - 17:50:42 CDT

Dear VMD users,

When I try to visualize my polymer PDB file in VMD, I see that for some reason VMD considers atom # 1 as atom # 0.

e.g.
When I try to visualize the bond between say atom 1 and atom 4 of the fragment in VMD, I specify "index 1 4" but I see the bond between the next atoms (between atom 2 and atom 5 ), so to visualize the bond between atom 1 and atom 4, I have to "index 0 3. Why is that happening ?

Any help will be greatly appreciated.

Thanks,
Ashar