AMBER Archive (2005)

Subject: AMBER: pdb file and xleap

From: Wai Keat Yam (yamwaikeat_at_yahoo.com)
Date: Tue Jul 19 2005 - 05:06:50 CDT


Dear Amber users,

Hello.

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
viewers.

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.

Regards,
Keat

                
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