Dear Amber,
One more question...
So, Leap adds the missing atoms in amino acids according to one
conformation stored in the template.
Why uses leap this conformation ? (Is it the most frequent rotamer ... ?
According to what reference article...?)
Thank you very much!
Marta Gomes
2013/2/21 Jason Swails <jason.swails.gmail.com>
> 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 Tue Mar 19 2013 - 03:30:03 PDT
