AMBER Archive (2008)

Subject: Re: AMBER: Imaging before HBond analysis?

From: Thomas Cheatham III (
Date: Fri Apr 11 2008 - 17:24:29 CDT

> I am wondering if the HBond function in ptraj (Amber version 9) implicitly
> handles PBC imaging considerations, or if an image command must be issued
> before the hbond command? The manual doesn't seem to state one or the other
> is the case.

It looks like imaging is disabled in the distance calculations of hbond so
imaging is likely necessary prior to the hbond command. I will fix this
to match default behavior (of implicitly imaging) [which will slow down
the command significantly unless "noimage" is specified] in an upcoming
AmberTools release and also will update the manual...

For now, image prior to doing the hbond command...

-- tec3
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