Re: [AMBER] Ptraj crashes and Hbond analysis

From: Kamali Sripathi <>
Date: Wed, 23 Mar 2011 14:16:15 -0400

Dear Dr. Cheatham,

I actually have a follow-up question as well: Could you (or anyone on the
Amber mailing list) point me to an archive email or online resource
explaining the difference between lifetime and occupancy? I ask this
question because I made a mistake with the "time" command. Each frame is 1ps
for my simulations, but I mistakenly set the "time" keyword to 200.

I was also wondering how to interpret the graphical schematic for lifetime.
I understand that each symbol represents an Hbond that is fulfilled for a
specific percentage, but what does that percentage mean, exactly? As in, the
"." sign represents 95-100% occupancy, but in the graphical schematic there
could be about 15 strung together.

I know there are plenty of lengthy answers in the AMBER mailing list
archive, but I just haven't been able to find them again.

Thank you all very much,

Kamali Sripathi

On Tue, Mar 22, 2011 at 7:33 PM, Thomas Cheatham III <> wrote:

> > 1) I'm experiencing a problem where I use ptraj scripts to analyze
> several
> > simulations of structures very similar to each other. The scripts mostly
> > work, but when I use this script for a certain few structures ptraj
> > consistently crashes. Has anyone else experienced this?
> There is insufficient information provided to comment.
> > 2) Could someone please point me to one of the emails that explain the
> > "time" keyword in the "hbond" command? I know there are several in-depth
> > explanations of this facility in the archive, but I haven't been able to
> > find them.
> The trajectory file only contains coordinates; there is no information on
> time or the interval of time between frames. Therefore this keyword
> allows specifying the "time" interval between frames, in picoseconds. If
> you have frames processed every 1 ps, "time 1.0" is appropriate. If every
> 100 ps, "time 100.0".
> --tec3
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Received on Wed Mar 23 2011 - 11:30:04 PDT
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