AMBER Archive (2003)

Subject: AMBER: Insight pdb file in xleap

From: Wayne Dawson (dawson_at_nih.go.jp)
Date: Thu Aug 07 2003 - 21:33:26 CDT

Mi-Kyung Seo wrote:

> I loaded pdb file made by Insight in Leap (Amber7.0) and use
> "bondByDistance" command to put in bonds using default criteria.
> However, some bonds are disconnected and structure is broken. Is
> pdb file made by Insight different from pdb format which can be
> loaded in leap?

Even for proteins, Insight adds a variety of idiosyncrasies to the pdb
files that Amber doesn't recognize. I found the best way is to just
keep ripping out all the Insight specific stuff until xleap stops
complaining when you save the *.crd file.

>From there, the best procedure I found was to follow something like
the example on page 55 of the Amber 7 manual (loadPdbusingSeq). But
then again, maybe you will just have to add the bonds manually.

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