Hi George,
you will have to choose one ... and remove the other "arbitrarily", or better
depending on the needs of your experiment. LEaP would otherwise possibly create
a strange structure with two residues in the same place or similar strange
things. The questions why there are two conformations at all ... is there realy
two conformations present in the crystal?
You can also simulate both structures simultaneously if you cannot decide and
have the resources. Maybe the conformations interconvert during MD.
Alex
________________________________
Von: George Tzotzos <gtzotzos.me.com>
An: AMBER Mailing List <amber.ambermd.org>
Gesendet: Dienstag, den 14. September 2010, 15:54:15 Uhr
Betreff: [AMBER] Residues with multiple conformations
Hi everybody,
I'd like to ask what is the best way to handle PDB files in which some of the
residues are shown in multiple conformations.
Does it make sense to keep one conformation only removing the others
arbitrarily. Or keep them all despite the warnings issued by LEAP.
Regards
George
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Received on Tue Sep 14 2010 - 08:00:03 PDT
