VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Wed Mar 16 2011 - 15:03:45 CDT

Hi Leila,

On Mar 12, 2011, at 3:19 AM, leila karami wrote:

> Hello,
>
> I want to calculate hydrogen bond lifetimes through trajectory.
>
> I started VMD then loaded trajectory (e.g. file.xyz and history), at last i selected Extensions: Analysis: Timeline from "VMD Main" window to calculate: Calc H-bonds, but it can’t show hydrogen bond lifetimes through trajectory.
>
> Time line couldn’t find a sequence in this molecule.
>
> Can Timeline recognize *.trr or *.xyz or HISTORY as input file?
>
>
>
> Best wishes,
>
>

        The Timeline plugin relies on common atom names to recognize parts of protein and amino acid residues. If you send me a a link to the problematic files, I'll have a look and try to see what's going wrong.

                Cheers,

                Barry 

-- 
Barry Isralewitz
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612
email: barryi_at_ks.uiuc.edu   http://www.ks.uiuc.edu/~barryi