On Thu, Feb 21, 2013 at 10:59 AM, Marta Perez
<marta.silva.perez.gmail.com>wrote:
> Dear Amber,
>
> I have un doubt related with the "Leap".
> In my structure I had some aminoacids with missing atoms and the "Leap"
> added the missing atoms according to residues templates.
> What this means?
The files in $AMBERHOME/dat/leap/lib has a table of all residues and it
lists the atoms in that residue (atom type, atom name, and charge, for
instance), and that residue is in a particular conformation (i.e., ONE
rotamer). If any atoms are missing, then it fills in the missing atoms
according to this ONE conformation stored in the 'template'.
The more atoms that tleap has to insert, the worse the starting structure
will likely be.
Hope this helps,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 21 2013 - 09:00:03 PST
