missing residues

From: Mark Hsieh <hsieh_at_abmaxis.com>
Date: Sun 5 May 2002 00:15:31 -0700


I'm trying to build a set of prmtop and inpcrd for a
pdb structure that's missing six loop residues in the
middle. I can read the coordinates and use the deletebond
to remove the artificially long bond but what's the best
way to handle such a case under minimization and MD? Is
there a strategy to artificially patch missing residues?

Do I need to build in the missing six residues or can I
get away by constraining the ends of the fragments? The
missing residues are far away from the region of interest.

Thank you,
Received on Sun May 05 2002 - 00:15:31 PDT
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