From: Steve Seibold <>
Date: Fri, 10 Aug 2007 16:17:47 -0400

Hello Amber

I tried to send the attachments, but after one hour they have not showed
up on the AMBER site and so, I am now sending the following message
without the attachments.


I have an unusual problem with xleap or when I make a pdb file using
"ambdpb". When I load my initial pdb file (p010A.pdb) into xleap and
save my topology and coordinate files WITHOUT water my output pdb files
are fine. However, if I add waters and follow the same procedure (i.e.
load p010A.pdb and make promtop and inpcrd files), I get very strange
placements of the "TER" command when I construct a pdb file using
"savepdb file file.pdb" or "ambpdb" commands. Basically it slices up my
protein and the heme.


When I use "desc mol" while using xleap the c-terminal and n-terminal
are fine with or without water. It is only when I write out a pdb file
that I get this problem.


Can someone tell what is going on? Has this happened to someone else?


Thanks, Steve






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Received on Sun Aug 12 2007 - 06:07:54 PDT
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