AMBER Archive (2003)

Subject: RE: AMBER: Insight pdb file in xleap

From: Yong Duan (yduan_at_udel.edu)
Date: Thu Aug 07 2003 - 18:35:03 CDT

This is likely related to the simple logic used in the bond recognition
method in Leap. You probably need to manually connect those broken
bonds.

Hope this helps ...

Good luck!

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Mi-Kyung Seo
Sent: Thursday, August 07, 2003 7:10 PM
To: amber_at_scripps.edu
Subject: AMBER: Insight pdb file in xleap

Hello Amber users,

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?

..........

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