Re: AMBER: PDB problems

From: Ilyas Yildirim <>
Date: Fri, 15 Jun 2007 18:30:45 -0400 (EDT)

xleap is useful to visualize the structure, explicitly. tleap is good, if
you write a shell script that creates structures using leap (or for any
other reason, which requires multiple use of leap.

For your .pdb question, if you see leap creating some extra atoms after
loading the .pdb (assuming that this .pdb file is taken from, or
assuming that the created atoms are not H-atoms), it is better to check
the .pdb file; to see what those atoms are. Sometimes, this happens to me
too; and the reason is because the loaded .lib files (which have all the
residue information when u load the force field you wanna use) do not have
atoms defined for those extra atoms.


On Fri, 15 Jun 2007, Taryn Hartley wrote:

> Is everyone who is running simulations in Amber building their structure in xleap or tleap??? Is there anyone who is using a structure from the Protein Data Bank? and if so.... are you having problems with atom types? Is there a command in AMBER that automatically converts atom types? -Taryn
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  Ilyas Yildirim
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Received on Sun Jun 17 2007 - 06:07:38 PDT
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