Did the xleap say it created a new atom type for that residue? If yes,
perhaps you have a differently named hydrogen atom in your pdb file. One
thing you can check is to load the pdb and edit it in xleap. If you look at
the structure and can find a small white circle close to that N-terminus, I
guess it's the reason.
Guanglei Cui
-----Original Message-----
From: Jake Isaacs [mailto:rjisaa0_at_pop.uky.edu]
Sent: Thursday, March 29, 2001 10:05 AM
To: AMBER list
Subject: LEaP adding an extra hydrogen to N-terminus
When I load a pdb file for a 2 subunit protein into LEaP, it adds a fourth
hydrogen to the N-terminal nitrogens. All hydrogens I need are already
present in the pdb, and the other three N-terminal hydrogens seem to be
correctly arranged in both N-terminal residues. Any idea whats going on and
how I can fix it? Shoud I just strip all the hydrogens and let LEaP add
them all back?
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Received on Thu Mar 29 2001 - 07:48:05 PST
