AMBER Archive (2009)
Subject: Re: [AMBER] problem from xleap
From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Fri Jul 31 2009 - 11:41:49 CDT
I only looked briefly but this does not look like a complete protein.
Many residues are missing, which leaves many regions unconnected.
Please be sure this is OK for what you want to do (e.g. for MD, the
resulting simulation may be quite different from how the receptor acts
in reality). You may wish to use a complete protein without gaps.
Leap joins together residues that are adjacent in the PDB file, even
if the bond length would be unrealistic. You can keep it from doing
this by inserting TER records in the PDB file between the residues
that need to be separated.
On Fri, Jul 31, 2009 at 10:38 AM, Qinghua Liao<fantasticqhl_at_yahoo.com> wrote:
> Dear amber users,
> I have a problem when using xleap. when I load the pdb file of receptor, then check it, it gives me those warnings that there are several bonds with a more than 10 angstroms bond length. The attachment file is the pdb file of receptor for you to check for me!
> I can't understand that. Could somebody tell me the reason? Any response will be highly appreciated!
> All the best!
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