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