VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Sat Mar 14 2015 - 19:21:08 CDT

Ashar,
Try "serial 1 4”
Also, take a look at VMD User Guide

Maxim

> On Mar 14, 2015, at 17:50, Arjun Sharma <arjunsharma83_at_gmail.com> wrote:
>
> 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
>
>