AMBER Archive (2002)

Subject: missing residues

From: Mark Hsieh (hsieh_at_abmaxis.com)
Date: Sun May 05 2002 - 02:15:31 CDT

Hi,

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,
Mark