AMBER Archive (2005)

Subject: AMBER: Leap task

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Nov 04 2005 - 05:44:39 CST

Dear Amber users,
    I would like to ask you if you have any idea how to deal with the
following situation:
    lets say I have a residue which has 4 equivalent atoms,named X1, X2,
X3 and X4. The problem arises when the X2 atom from the pdb file to be
loaded corresponds to the X3 atom in the leap internal library of that
residue (and similarly X1 to X4).
    So I would like to tell Leap that X1=X2=X3=X4, so that leap could
exchange the name of the X2 atom to X3 (or X1 to X4), whenever it
encounters an X2 (X1) atom that corresponds to X3 (X4) in its internal
library.
    The second problem is that the name X2 may be present in other
residues where is not equivalent to X3 and thus, it should be changed
only in the residue where I have these X1-X2-X3-X4 equivalent atoms.

    If somebody has any idea how to deal with this problem, I would
appreciate an answer.

Best wishes
vlad

P.S1. Of course an obvious thing would be to change the names in such a
way that the problems dissapears. That might be ok if I would have only
1 pdb file to load but what if there are many different pdbs, in some X1
corresponding the the X4 in the library, in others X1 corresponding to
X3 ... and so on.

P.S2. I hope I stated the problem clear enough ... Please let me know if
that's not the case ... 

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Villa Bosch
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de

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