AMBER: pdb file and xleap

From: Wai Keat Yam <>
Date: Tue, 19 Jul 2005 03:06:50 -0700 (PDT)

Dear Amber users,


I have ran a few minimizations using sander for a very
large biomolecule with many bad contacts. After the
second minimization, I decided to check my structure
before proceeding further minimization. I used the
"ambpdb" command to create pdb file from the rst file
and its prmtop file as well.

When I tried to view the pdb file (that were created
using ambpdb) using viewer (VMD, insightII), I found
that the structure has a lot of broken bonds. Then
when I view it again in xleap, the structure looks ok
without any broken bonds like the one I saw in

So, which one should I trust? the viewer? or xleap??
anyone can help to explain this? should I proceed
further minimization?

Please help.

Thanks a lot.


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Received on Tue Jul 19 2005 - 11:53:00 PDT
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