Re: [AMBER] question about bond command

From: Philippe Pinard <>
Date: Thu, 22 Jul 2010 14:41:26 -0700 (PDT)


I am still confused whether or not I should use the bond command to bond the
residues i defined with antechamber inside my pdb molecule. This is because in
tutorial 1, it says "xleap is fairly simple in that it expects that all residues
in the pdb file are connected in the order in which they are listed unless they
are separated by a "TER" card (i.e. a single line that says "TER") and that the
first residue read in is "tail only" and the last residue is "head only", In a
conventional pdb file we do not use bond command between different residues,

Why should I use bond command for my constructed by hand pdb file?

My other concern, when i try the desc command on my 4 defined residues all have
tail and head. Is this normal? The thing is all my residues "RESD" are terminal
groups, so I guess they need to have just head. If this is correct how to
eliminate tail in "RESD".

Thanks for any help

From: Bill Ross <ross.cgl.ucsf.EDU>
Sent: Thu, July 22, 2010 8:38:28 PM
Subject: Re: [AMBER] question about bond command

> concerning connect command: my residu connects to others using 5 atoms.
> I never used connect command, is this to define head and tail?

You would use the 'set' command I believe, to set connectX atoms
and head=connect0 and tail=connect1. This would be when defining
your residues before saveoff. Then after loadpdb you would use
the bond cmd to join the relevant atoms defined with connectX
property (X in {0, 1, 2, ...}).

See the tutorials for details.


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