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
____________________________________________________
Start your day with Yahoo! - make it your home page
http://www.yahoo.com/r/hs
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|